Phylogenomics of Pyrenodesmia
Fernando Fernandez Mendoza
7/6/2021
1 Introduction
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1.1 Data input
The first parts of the script retrieve data sources,
## Registered S3 method overwritten by 'ggtree':
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## identify.gg ggfun## ggtree v3.2.1 For help: https://yulab-smu.top/treedata-book/
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## If you use ggtree in published research, please cite the most appropriate paper(s):
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## 1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96
## 2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution. 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
## 3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628##
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## pull## Loading required package: rjson2 The phylogenomic dataset
synopsis<-read.delim2("/Users/Fernando/Desktop/01_paper_sanger_drive/genome_stats.txt")
kable(synopsis)| Species | Assembly.Size | Largest.Scaffold | Average.Scaffold | Num.Scaffolds | Scaffold.N50 | Percent.GC | Num.Genes | Num.Proteins | Num.tRNA | Unique.Proteins | Prots.atleast.1.ortholog | Single.copy.orthologs |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Xanthoria_parietina | 31900637 | 3929677 | 817965 | 39 | 1731186 | 49.73 | 9488 | 9431 | 57 | 1390 | 8041 | 3021 |
| Gyalolechia_flavorubescens | 34468235 | 2816824 | 957451 | 36 | 1693300 | 41.79 | 9880 | 9823 | 57 | 1572 | 8251 | 3021 |
| Pyrenodesmia_erodens | 41851374 | 2781653 | 1162538 | 36 | 1704480 | 44.05 | 9416 | 9370 | 46 | 386 | 8984 | 3021 |
| Pyrenodesmia X2 | 43348608 | 1837403 | 240826 | 180 | 376967 | 42.31 | 10320 | 10272 | 48 | 474 | 9798 | 3021 |
| Pyrenodesmia X3 | 37275908 | 1320638 | 248506 | 150 | 419601 | 45.53 | 9898 | 9850 | 48 | 212 | 9638 | 3021 |
| Pyrenodesmia X4 | 41798408 | 2794185 | 435400 | 96 | 731853 | 43.38 | 10056 | 10010 | 46 | 319 | 9691 | 3021 |
| Pyrenodesmia X5 | 34428752 | 1072771 | 180255 | 191 | 312859 | 47.01 | 9695 | 9652 | 43 | 278 | 9374 | 3021 |
| Pyrenodesmia X6 | 35186806 | 1032653 | 129363 | 272 | 189335 | 45.97 | 9112 | 9070 | 42 | 281 | 8789 | 3021 |
| Pyrenodesmia X7 | 40660310 | 1499439 | 280416 | 145 | 429105 | 42.90 | 9722 | 9625 | 97 | 256 | 9369 | 3021 |
| Pyrenodesmia X8 | 39614804 | 1433674 | 309491 | 128 | 468261 | 44.39 | 10050 | 10006 | 44 | 223 | 9783 | 3021 |
| Pyrenodesmia X9 | 43659406 | 1131763 | 263008 | 166 | 423490 | 42.62 | 9808 | 9762 | 46 | 389 | 9371 | 3021 |
| Pyrenodesmia Y1 | 34734309 | 759625 | 149074 | 233 | 219802 | 47.43 | 10006 | 9960 | 46 | 342 | 9615 | 3021 |
| Pyrenodesmia Y2 | 50248555 | 1799656 | 380671 | 132 | 745020 | 39.44 | 9228 | 9178 | 50 | 330 | 8848 | 3021 |
| Pyrenodesmia Y3 | 41509736 | 1945962 | 334756 | 124 | 571577 | 44.22 | 9989 | 9943 | 46 | 258 | 9685 | 3021 |
| Pyrenodesmia Y4 | 31441282 | 797770 | 40206 | 782 | 65651 | 44.38 | 8107 | 8069 | 38 | 420 | 7646 | 3021 |
| Pyrenodesmia Y5 | 41119244 | 1867145 | 345540 | 119 | 583469 | 43.92 | 9939 | 9873 | 66 | 202 | 9671 | 3021 |
| Pyrenodesmia Y6 | 39489925 | 1532758 | 278098 | 142 | 426766 | 43.50 | 9955 | 9908 | 47 | 237 | 9671 | 3021 |
| Pyrenodesmia Y7 | 43221143 | 1712518 | 294021 | 147 | 584803 | 42.04 | 9960 | 9883 | 77 | 329 | 9552 | 3021 |
| Pyrenodesmia Y8 | 43948905 | 1539690 | 240158 | 183 | 418742 | 43.08 | 10115 | 10058 | 57 | 573 | 9480 | 3021 |
| Pyrenodesmia Y9 | 38308288 | 2270234 | 517680 | 74 | 905955 | 44.72 | 9585 | 9448 | 137 | 328 | 9120 | 3021 |
| Pyrenodesmia Y10 | 38841502 | 1412088 | 227143 | 171 | 360919 | 45.12 | 10123 | 10075 | 48 | 267 | 9808 | 3021 |
| Pyrenodesmia Y11 | 40472199 | 1156999 | 249828 | 162 | 349194 | 43.08 | 10018 | 9971 | 47 | 319 | 9652 | 3021 |
| Pyrenodesmia Y12 | 32661819 | 560224 | 102388 | 319 | 183671 | 48.72 | 10022 | 9976 | 46 | 473 | 9501 | 3021 |
| Pyrenodesmia Y13 | 40315950 | 1335582 | 180789 | 223 | 285734 | 44.40 | 9041 | 8986 | 55 | 295 | 8691 | 3021 |
| Pyrenodesmia Y14 | 39991836 | 1021580 | 186009 | 215 | 319254 | 43.42 | 9817 | 9773 | 44 | 365 | 9408 | 3021 |
synopsis_backup<-synopsis
synopsis<-synopsis[-c(1,2),]ggplot(synopsis,aes(x=1,y=Assembly.Size))+geom_violin(fill = "#6001A655")+geom_point(position = position_jitter(seed = 1, width = 0.1),col = (1+as.numeric(synopsis$Species=="Pyrenodesmia_erodens")))+ labs (title="Assembly size") + theme_bw()
ggplot(synopsis,aes(x=1,y=Scaffold.N50))+geom_violin(fill = "#6001A655")+geom_point(position = position_jitter(seed = 1, width = 0.1),col = (1+as.numeric(synopsis$Species=="Pyrenodesmia_erodens")))+ labs (title="N50") + theme_bw()
ggplot(synopsis,aes(x=1,y=as.numeric(Percent.GC)))+geom_violin(fill = "#6001A655")+geom_point(position = position_jitter(seed = 1, width = 0.1),col = (1+as.numeric(synopsis$Species=="Pyrenodesmia_erodens")))+ labs (title="GC content") + theme_bw()
ggplot(synopsis,aes(x=1,y=Num.Genes))+geom_violin(fill = "#6001A655")+geom_point(position = position_jitter(seed = 1, width = 0.1),col = (1+as.numeric(synopsis$Species=="Pyrenodesmia_erodens")))+ labs (title="Number of genes") + theme_bw()
ggplot(synopsis,aes(x=1,y=Unique.Proteins))+geom_violin(fill = "#6001A655")+geom_point(position = position_jitter(seed = 1, width = 0.1),col = (1+as.numeric(synopsis$Species=="Pyrenodesmia_erodens")))+ labs (title="Unique proteins") + theme_bw()
ggplot(synopsis,aes(x=synopsis$Assembly.Size,y=Scaffold.N50))+geom_point(position = position_jitter(seed = 1, width = 0.1),col = (1+as.numeric(synopsis$Species=="Pyrenodesmia_erodens")))+ labs (title="Assembly size") + theme_bw()## Warning: Use of `synopsis$Assembly.Size` is discouraged. Use `Assembly.Size`
## instead.
3 Description of the Pyrenodesmia erodens genome
library(karyoploteR)## Loading required package: regioneR## Loading required package: GenomicRanges## Loading required package: stats4## Loading required package: BiocGenerics##
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## IQR, mad, sd, var, xtabs## The following objects are masked from 'package:base':
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## anyDuplicated, append, as.data.frame, basename, cbind, colnames,
## dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
## grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
## order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
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## collapse## Loading required package: GenomeInfoDblibrary(GenomicRanges)
repbase<-read.delim("/Users/Fernando/Desktop/01_paper_sanger_drive/P_erodens_sorted_relimited.fas.out",header = TRUE,sep="\t")
repbase<-repbase[!(is.na(repbase$start)),]
repbase$strand[repbase$strand=="C"]<-"-"
repetitive_sequences<-repbase[repbase$class=="Simple_repeat",]
mobile_elements<-repbase[repbase$class!="Simple_repeat",]
mobile_elements<-mobile_elements[mobile_elements$class!="Low_complexity",]
# Smith Watermann score
mobile_elements<-mobile_elements[mobile_elements$SW_score>=100,]
#mobile_elements<-mobile_elements[mobile_elements$class!="Unknown",]
#mobile_elements<-mobile_elements[mobile_elements$class!="Unspecified",]
dna1<-makeGRangesFromDataFrame(mobile_elements[mobile_elements$class%in%c("DNA/hAT-Ac","DNA/MULE-MuDR"),],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="query_seq",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
ltrcopia<-makeGRangesFromDataFrame(mobile_elements[mobile_elements$class=="LTR/Copia",],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="query_seq",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
ltrgypsy<-makeGRangesFromDataFrame(mobile_elements[mobile_elements$class=="LTR/Gypsy",],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="query_seq",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
ltrNgaro<-makeGRangesFromDataFrame(mobile_elements[mobile_elements$class=="LTR/Ngaro",],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="query_seq",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
helitron<-makeGRangesFromDataFrame(mobile_elements[mobile_elements$class=="RC/Helitron",],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="query_seq",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
telomeres<-repetitive_sequences[repetitive_sequences$rpeat=="(AACCCT)n",]
telomeres<-makeGRangesFromDataFrame(telomeres,
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="query_seq",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
#repetitive_sequences<-repetitive_sequences[repetitive_sequences$rpeat!="(AACCCT)n",]
repetitive_sequences<-makeGRangesFromDataFrame(repetitive_sequences,
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="query_seq",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
mobile_elements<-makeGRangesFromDataFrame(mobile_elements,
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="query_seq",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
ranges_genes2<-makeGRangesFromDataFrame(genes2,
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="scaffold",
start.field="start",
end.field="end",
starts.in.df.are.0based=FALSE)
pe.genome <- toGRanges(data.frame(chr=names(pe_genome), start=rep(1,length(pe_genome)), end=sapply(pe_genome,length)))3.1 Graphical description of the genome
kp <- plotKaryotype(genome = pe.genome, plot.type= 2)
kpPlotRegions(kp, data=paste(lrar$Name,":",lrar$Start+1,"-",lrar$End+1,sep=""),data.panel = 2,
col=grey(0.3), r0=-0.35, r1=-0.1, avoid.overlapping=FALSE)
dens_Me<-kpPlotDensity(kp, data=mobile_elements,data.panel = 1,col=grey(0.3), r0=0, r1=1,window.size=50000)
coding_dens<-kpPlotDensity(kp, ranges_genes2, col="#6001A655",data.panel = 1, r0=0, r1=1, window.size = 50000)
kpPlotRegions(kp, data=repetitive_sequences,data.panel = 2,col=grey(0.2), r0=0, r1=0.3, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=dna1,data.panel = 2,col=spectrum[5], r0=0.3, r1=0.6, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=ltrcopia,data.panel = 2,col=spectrum[25], r0=0, r1=0.3, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=ltrgypsy,data.panel = 2,col=spectrum[10], r0=0, r1=0.3, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=ltrNgaro,data.panel = 2,col=spectrum[15], r0=0, r1=0.3, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=helitron,data.panel = 2,col=spectrum[10], r0=0.3, r1=0.6, avoid.overlapping=FALSE)
3.2 Cluster Large RIP Affected Regions based on their content in repeatable elements
In higher eukaryotes the TE content has been shown to be directly related to the effective population size of the host organism. Lynch M, Conery JS (2003) The origins of genome complexity. Science 302: 1401–1404
tabulate_rep_lrar<-table(repbase$class)
tabulate_rep_lrar<-rbind(tabulate_rep_lrar,tabulate_rep_lrar)
for (LRAR in c(1:dim(lrar)[1]))
{
foo.scaffold<-lrar[LRAR,1]
foo.start<-lrar[LRAR,2]
foo.end<-lrar[LRAR,3]
foo.repbase<-repbase[repbase$query_seq==foo.scaffold&repbase$start>=foo.start&repbase$end<=foo.end,]
tabulate_rep_lrar<-rbind(tabulate_rep_lrar,table(foo.repbase$class)[colnames(tabulate_rep_lrar)])
}
tabulate_rep_lrar<-tabulate_rep_lrar[-1,]
tabulate_rep_lrar[is.na(tabulate_rep_lrar)]<-0
tabulate_rep_lrar1<-tabulate_rep_lrar[1,]
tabulate_rep_lrar<-tabulate_rep_lrar[-1,]
tabulate_rep_lrar<-cbind(lrar,tabulate_rep_lrar/lrar$Size)
Coding_regions<-NULL
tabulate_regions<-rbind(tabulate_rep_lrar1,tabulate_rep_lrar1)
#tabulate_regions[]<-0
for (LRAR in c(levels(factor(lrar[,1]))))
{
foo.lrar<-lrar[lrar[,1]==LRAR,]
Coding_regions<-rbind(Coding_regions,cbind(Scaf=LRAR,Start=c(0,foo.lrar$End),End=c(foo.lrar$Start,length(pe_genome[[LRAR]]))))
}
Coding_regions<-Coding_regions[!(Coding_regions[,2]==0&Coding_regions[,3]==0),]
for (LRAR in c(1:dim(Coding_regions)[1]))
{
foo.scaffold<-Coding_regions[LRAR,1]
foo.start<-Coding_regions[LRAR,2]
foo.end<-Coding_regions[LRAR,3]
foo.repbase<-repbase[repbase$query_seq==foo.scaffold&repbase$start>=foo.start&repbase$end<=foo.end,]
tabulate_regions<-rbind(tabulate_regions,table(foo.repbase$class)[colnames(tabulate_regions)])
rm (foo.scaffold)
rm (foo.start)
rm (foo.end)
}
tabulate_regions<-tabulate_regions[-c(1,2),]
tabulate_regions[is.na(tabulate_regions)]<-0
Coding_regions<-data.frame(Coding_regions[,1],matrix(as.numeric(Coding_regions[,-1]),ncol = ncol(Coding_regions)-1),tabulate_regions)
Coding_regions[,4:13]<-Coding_regions[,4:13]/(Coding_regions[,3]-Coding_regions[,2])
Coding_regions<-Coding_regions[(Coding_regions[,3]-Coding_regions[,2])!=0,]3.3 Cluster Large RIP Affected Regions based on their LTR content
grupos<-Mclust(tabulate_rep_lrar[,c(13:15,18)],1:6)kp <- plotKaryotype(genome = pe.genome,plot.type=2,chromosomes=c("scaffold_11","scaffold_12","scaffold_13","scaffold_14","scaffold_21","scaffold_23"))
kpPlotRegions(kp, data=paste(lrar$Name,":",lrar$Start+1,"-",lrar$End+1,sep=""),data.panel = 2,
col=grey(0:0.5)[grupos$classification], r0=-0.35, r1=-0.1, avoid.overlapping=FALSE)
kpPlotDensity(kp, data=mobile_elements,data.panel = 1,col=grey(0.3), r0=0, r1=1,window.size=50000)
kpPlotDensity(kp, ranges_genes2, col="#6001A655",data.panel = 1, r0=0, r1=1, window.size = 50000)
kpPlotRegions(kp, data=repetitive_sequences,data.panel = 2,col=grey(0.2), r0=0, r1=0.3, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=dna1,data.panel = 2,col=spectrum[5], r0=0.3, r1=0.6, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=ltrcopia,data.panel = 2,col=spectrum[25], r0=0, r1=0.3, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=ltrgypsy,data.panel = 2,col=spectrum[10], r0=0, r1=0.3, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=ltrNgaro,data.panel = 2,col=spectrum[15], r0=0, r1=0.3, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=helitron,data.panel = 2,col=spectrum[10], r0=0.3, r1=0.6, avoid.overlapping=FALSE)
#, border=spectrum[10], r0=1, r1=-0.5, avoid.overlapping=FALSE)ggplot(data.frame(lrars=tabulate_rep_lrar[,10],class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title=colnames(tabulate_rep_lrar)[10]) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
ggplot(data.frame(lrars=tabulate_rep_lrar[,11],class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title=colnames(tabulate_rep_lrar)[11]) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
ggplot(data.frame(lrars=tabulate_rep_lrar[,12],class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title=colnames(tabulate_rep_lrar)[12]) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
ggplot(data.frame(lrars=tabulate_rep_lrar[,13],class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title=colnames(tabulate_rep_lrar)[13]) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
ggplot(data.frame(lrars=tabulate_rep_lrar[,14],class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title=colnames(tabulate_rep_lrar)[14]) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
ggplot(data.frame(lrars=tabulate_rep_lrar[,15],class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title=colnames(tabulate_rep_lrar)[15]) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
ggplot(data.frame(lrars=tabulate_rep_lrar[,16],class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title=colnames(tabulate_rep_lrar)[16]) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
ggplot(data.frame(lrars=tabulate_rep_lrar[,17],class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title=colnames(tabulate_rep_lrar)[17]) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
ggplot(data.frame(lrars=tabulate_rep_lrar[,18],class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title=colnames(tabulate_rep_lrar)[18]) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
ggplot(data.frame(lrars=tabulate_rep_lrar[,19],class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title=colnames(tabulate_rep_lrar)[19]) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
##
Centromeres
Based on only 16 kb of sequence, it was concluded that Neurospora centromeres are composed of degenerate transposons, mostly retrotransposons, and simple sequence repeats. The degenerate nature of the transposons is due to the action of a premeiotic process called “Repeat-Induced Point mutation” (RIP), which through an unknown mechanism recognizes repeated DNA and mutates both copies, yielding numerous C:T and G:A transition mutations (Cambareri et al., 1989, Selker, 1990). RIP will continue in successive sexual cycles until sequence identity between two copies decreases below ~85% but it will begin again if such regions become re-duplicated (Cambareri et al., 1991). Presumably these cycles of duplication and mutagenesis can continue until no Cs remain. Combined with potential gene conversion or recombination events, RIP appears to provide an interesting mechanism for diversification of centromeric DNA in many filamentous fungi.
lrar_clust1<-makeGRangesFromDataFrame(tabulate_rep_lrar[grupos$classification==1,],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="Name",
start.field="Start",
end.field="End",
starts.in.df.are.0based=FALSE)
lrar_clust2<-makeGRangesFromDataFrame(tabulate_rep_lrar[grupos$classification==2,],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="Name",
start.field="Start",
end.field="End",
starts.in.df.are.0based=FALSE)
lrar_clust3<-makeGRangesFromDataFrame(tabulate_rep_lrar[grupos$classification==3,],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="Name",
start.field="Start",
end.field="End",
starts.in.df.are.0based=FALSE)
lrar_clust4<-makeGRangesFromDataFrame(tabulate_rep_lrar[grupos$classification==4,],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="Name",
start.field="Start",
end.field="End",
starts.in.df.are.0based=FALSE)
kp <- plotKaryotype(genome = pe.genome, plot.type= 2)
kpPlotRegions(kp, data=lrar_clust1,data.panel = 1,col=spectrum[5], r0=0, r1=0.3, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=lrar_clust2,data.panel = 1,col=spectrum[10], r0=0.3, r1=0.6, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=lrar_clust3,data.panel = 2,col=spectrum[15], r0=0, r1=0.3, avoid.overlapping=FALSE)
kpPlotRegions(kp, data=lrar_clust4,data.panel = 2,col=spectrum[25], r0=0.3, r1=0.6, avoid.overlapping=FALSE)
3.4 Loss of synteny across the genome
#meko<-"| |"
#lost_out<-NULL
#for (FILE in list.files("/Users/Fernando/Desktop/01_paper_sanger_drive/06_Synteny/all.html/")[-1])
#{
#salida<-NULL
#prueba<-XML::readHTMLTable(paste("/Users/Fernando/Desktop/01_paper_sanger_drive/06_Synteny/all.html/",FILE,sep=""))
#foo<-grep("Pyrenodesmiaerodens_",prueba[[1]])
# if(length(foo)!=0)
# {
# prueba<-prueba[[1]][,c(1,2,foo)]
# for (i in 3:dim(prueba)[2])
# {
# salida<-rbind(salida,as.matrix(prueba[min(grep("Pyrenodesmiaerodens",prueba[,i])):max(grep("Pyrenodesmiaerodens",prueba[,i])),c(1,2,i)]))
# }
# salida[,3]<-gsub("-T1","",salida[,3])
# salida<-cbind(salida,genes2[salida[,3],c("scaffold","start","end")])
# for (i in 1:dim(salida)[1])
# {
# if (salida[i,3]==meko)
# {
# salida[i,3]<-paste(salida[i-1,3],"lost",sep = "-")
# scaff_pre<-salida[i-1,4]
# j<-i
# while(is.na(salida[j,4]))
# {
# j=j+1
# }
# scaff_post<-salida[j,4]
# if(!(is.na(scaff_pre)|is.na(scaff_post)))
# {
# if(scaff_pre==scaff_post)
# {
# salida[i,4]<-scaff_pre
# salida[i,5]<-as.integer(mean(c(as.numeric(salida[j,5]),as.numeric(salida[i-1,5]))))
# salida[i,6]<-as.numeric(salida[i,5])+100
# }
# }
# }
# }
# salida<-salida[sapply(strsplit(salida[,3],"-"),`[`,2)=="lost"&!is.na(sapply(strsplit(salida[,3],"-"),`[`,2)),]
# if(dim(salida)[1]>0)
# {
# lost_out<-rbind(lost_out,cbind(FILE,unname(salida)))
# }
# }
#}
#colnames(lost_out)<-c("file","depth","ref","name","scaffold","start","end")#lost_out<-lost_out[grep("Pyrenodesmiaerodens",lost_out$name),]
#save(lost_out,file="/Users/Fernando/Desktop/01_paper_sanger_drive/synteny.Rdata")
load("/Users/Fernando/Desktop/01_paper_sanger_drive/synteny.Rdata")
lost_genes<-melt(strsplit(ogs$V5,", "))
rownames(lost_genes)<-lost_genes[,1]
foo<-table(lost_genes$L1)
lost_genes<-lost_genes[lost_genes$L1%in%names(foo)[foo>=10],1]
lost_genes<-lost_out[lost_out$ref%in%lost_genes,]
lost_genes<-makeGRangesFromDataFrame(lost_genes,
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="scaffold",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
kp <- plotKaryotype(genome = pe.genome, plot.type= 2)
kpPlotRegions(kp, data=paste(lrar$Name,":",lrar$Start+1,"-",lrar$End+1,sep=""),data.panel = 2,
col=grey(0.3), r0=-0.35, r1=-0.1, avoid.overlapping=FALSE)
fer<-kpPlotDensity(kp, ranges_genes2, col="#6001A655",data.panel = 1, r0=0, r1=1, window.size = 50000)
cobol<-kpPlotDensity(kp,lost_genes, col=spectrum[10],data.panel = 1, r0=0, r1=1.5, window.size = 50000)
trans<-kpPlotDensity(kp, data=mobile_elements,data.panel = 2,col=grey(0.3), r0=0, r1=1,window.size=50000)
3.5 Detail of disrupted scaffolds
detail <- plotKaryotype(genome = pe.genome,plot.type=1,chromosomes=c("scaffold_11","scaffold_12","scaffold_13","scaffold_14","scaffold_21","scaffold_23"))
kpPlotRegions(detail, data=paste(lrar$Name,":",lrar$Start+1,"-",lrar$End+1,sep=""),data.panel = 2,
col=grey(0.3), r0=-0.35, r1=-0.1, avoid.overlapping=FALSE)
#kpPlotDensity(kp,lost_genes, col=spectrum[10],data.panel = 1, r0=0, r1=1, window.size = 50000)
kpPlotDensity(detail, ranges_genes2, col="#6001A655",data.panel = 1, r0=0, r1=1, window.size = 10000)
kpPlotDensity(detail,lost_genes, col=spectrum[10],data.panel = 1, r0=0, r1=1, window.size = 10000)## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_21
## - in 'y': scaffold_1, scaffold_10, scaffold_15, scaffold_16, scaffold_17, scaffold_18, scaffold_19, scaffold_2, scaffold_20, scaffold_22, scaffold_24, scaffold_25, scaffold_26, scaffold_28, scaffold_29, scaffold_3, scaffold_30, scaffold_32, scaffold_33, scaffold_4, scaffold_5, scaffold_6, scaffold_7, scaffold_8, scaffold_9
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
3.5.1 Influence of the density of transposable elements and overall coding density on loss of synteny
anova(glm(cobol$latest.plot$computed.values$density~fer$latest.plot$computed.values$density*trans$latest.plot$computed.values$density, family = poisson))## Analysis of Deviance Table
##
## Model: poisson, link: log
##
## Response: cobol$latest.plot$computed.values$density
##
## Terms added sequentially (first to last)
##
##
## Df
## NULL
## fer$latest.plot$computed.values$density 1
## trans$latest.plot$computed.values$density 1
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 1
## Deviance
## NULL
## fer$latest.plot$computed.values$density 1363.23
## trans$latest.plot$computed.values$density 5.65
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 12.48
## Resid. Df
## NULL 857
## fer$latest.plot$computed.values$density 856
## trans$latest.plot$computed.values$density 855
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 854
## Resid. Dev
## NULL 9003.6
## fer$latest.plot$computed.values$density 7640.4
## trans$latest.plot$computed.values$density 7634.8
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 7622.3summary(glm(cobol$latest.plot$computed.values$density~fer$latest.plot$computed.values$density*trans$latest.plot$computed.values$density, family = poisson))##
## Call:
## glm(formula = cobol$latest.plot$computed.values$density ~ fer$latest.plot$computed.values$density *
## trans$latest.plot$computed.values$density, family = poisson)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -5.126 -2.854 -1.583 0.641 16.957
##
## Coefficients:
## Estimate
## (Intercept) 0.2801911
## fer$latest.plot$computed.values$density 0.0867651
## trans$latest.plot$computed.values$density -0.0135070
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 0.0010261
## Std. Error
## (Intercept) 0.0899817
## fer$latest.plot$computed.values$density 0.0053204
## trans$latest.plot$computed.values$density 0.0034140
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 0.0002946
## z value
## (Intercept) 3.114
## fer$latest.plot$computed.values$density 16.308
## trans$latest.plot$computed.values$density -3.956
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 3.483
## Pr(>|z|)
## (Intercept) 0.001847
## fer$latest.plot$computed.values$density < 2e-16
## trans$latest.plot$computed.values$density 7.61e-05
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 0.000497
##
## (Intercept) **
## fer$latest.plot$computed.values$density ***
## trans$latest.plot$computed.values$density ***
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 9003.6 on 857 degrees of freedom
## Residual deviance: 7622.3 on 854 degrees of freedom
## AIC: 8956.4
##
## Number of Fisher Scoring iterations: 6plot(glm(cobol$latest.plot$computed.values$density~fer$latest.plot$computed.values$density*trans$latest.plot$computed.values$density, family = poisson))
boxplot(cobol$latest.plot$computed.values$density~fer$latest.plot$computed.values$density)
boxplot(cobol$latest.plot$computed.values$density~trans$latest.plot$computed.values$density)
###
Taking regions with null gene density to implicitely eliminate the
effect of centromeric regions and LRARs.
plot(glm(cobol$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]~fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]*trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0], family = poisson))
boxplot(cobol$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]~fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0])
boxplot(cobol$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]~trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0])
3.5.2 Explicitely eliminating Subtelomeric regions
To eliminate subtelomeric regions we substracted 0.30Mbp from each side of the scaffolds where Telomeric motif repeats have been identified.
telomere_locs<-rbind(cbind(paste("scaffold",c(1:13,15,19:21,25,30,34),sep="_"),0,250000),cbind(paste("scaffold",c(1:7,9:12,14:18,22,25:29,32,33),sep="_"),sapply(pe_genome[paste("scaffold",c(1:7,9:12,14:18,22,25:29,32,33),sep="_")],length)-250000,sapply(pe_genome[paste("scaffold",c(1:7,9:12,14:18,22,25:29,32,33),sep="_")],length)))
colnames(telomere_locs)<-c("scaffold","start","end")
telomere_locs<-data.frame(scaffold=telomere_locs[,1],start=as.numeric(telomere_locs[,2]),end=as.numeric(telomere_locs[,3]))
telomere_locs$start[telomere_locs$start<0]<-0
telomere_locs$end[telomere_locs$end>sapply(pe_genome[telomere_locs$scaffold],length)]<-sapply(pe_genome[telomere_locs$scaffold],length)[telomere_locs$end>sapply(pe_genome[telomere_locs$scaffold],length)]
telomere_locs<-makeGRangesFromDataFrame(telomere_locs,
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="scaffold",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
kp <- plotKaryotype(genome = pe.genome, plot.type= 2)
kpPlotRegions(kp, telomere_locs,data.panel = 2,col=grey(0.3), r0=-0.35, r1=-0.1, avoid.overlapping=FALSE)
fer<-kpPlotDensity(kp, GenomicRanges::setdiff(ranges_genes2,telomere_locs), col="#6001A655",data.panel = 1, r0=0, r1=1, window.size = 50000)
cobol<-kpPlotDensity(kp,GenomicRanges::setdiff(lost_genes,telomere_locs), col=spectrum[10],data.panel = 1, r0=0, r1=1.5, window.size = 50000)## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_21, scaffold_27, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).trans<-kpPlotDensity(kp, GenomicRanges::setdiff(mobile_elements,telomere_locs),data.panel = 2,col=grey(0.3), r0=0, r1=1,window.size=50000)
3.5.3 Influence of the density of transposable elements and overall coding density on loss of synteny
summary(glm(cobol$latest.plot$computed.values$density~fer$latest.plot$computed.values$density*trans$latest.plot$computed.values$density, family = poisson))##
## Call:
## glm(formula = cobol$latest.plot$computed.values$density ~ fer$latest.plot$computed.values$density *
## trans$latest.plot$computed.values$density, family = poisson)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -3.1237 -1.1386 -0.6811 -0.1890 7.9254
##
## Coefficients:
## Estimate
## (Intercept) -1.9283601
## fer$latest.plot$computed.values$density 0.1393210
## trans$latest.plot$computed.values$density 0.0311400
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density -0.0004145
## Std. Error
## (Intercept) 0.1404064
## fer$latest.plot$computed.values$density 0.0085091
## trans$latest.plot$computed.values$density 0.0052655
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 0.0005365
## z value
## (Intercept) -13.734
## fer$latest.plot$computed.values$density 16.373
## trans$latest.plot$computed.values$density 5.914
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density -0.773
## Pr(>|z|)
## (Intercept) < 2e-16
## fer$latest.plot$computed.values$density < 2e-16
## trans$latest.plot$computed.values$density 3.34e-09
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 0.44
##
## (Intercept) ***
## fer$latest.plot$computed.values$density ***
## trans$latest.plot$computed.values$density ***
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 2565.8 on 857 degrees of freedom
## Residual deviance: 1916.8 on 854 degrees of freedom
## AIC: 2685.2
##
## Number of Fisher Scoring iterations: 6anova(glm(cobol$latest.plot$computed.values$density~fer$latest.plot$computed.values$density*trans$latest.plot$computed.values$density, family = poisson))## Analysis of Deviance Table
##
## Model: poisson, link: log
##
## Response: cobol$latest.plot$computed.values$density
##
## Terms added sequentially (first to last)
##
##
## Df
## NULL
## fer$latest.plot$computed.values$density 1
## trans$latest.plot$computed.values$density 1
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 1
## Deviance
## NULL
## fer$latest.plot$computed.values$density 608.96
## trans$latest.plot$computed.values$density 39.42
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 0.60
## Resid. Df
## NULL 857
## fer$latest.plot$computed.values$density 856
## trans$latest.plot$computed.values$density 855
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 854
## Resid. Dev
## NULL 2565.8
## fer$latest.plot$computed.values$density 1956.8
## trans$latest.plot$computed.values$density 1917.4
## fer$latest.plot$computed.values$density:trans$latest.plot$computed.values$density 1916.8plot(glm(cobol$latest.plot$computed.values$density~fer$latest.plot$computed.values$density*trans$latest.plot$computed.values$density, family = poisson))
boxplot(cobol$latest.plot$computed.values$density~fer$latest.plot$computed.values$density)
boxplot(cobol$latest.plot$computed.values$density~trans$latest.plot$computed.values$density)
3.5.4 Taking regions with null gene density to implicitely eliminate the effect of centromeric regions and LRARs.
summary(glm(cobol$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]~fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]*trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0], family = poisson))##
## Call:
## glm(formula = cobol$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density !=
## 0] ~ fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density !=
## 0] * trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density !=
## 0], family = poisson)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.1187 -1.2252 -0.5951 0.5425 5.3942
##
## Coefficients:
## Estimate
## (Intercept) 0.6652425
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 0.0358652
## trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 0.0018219
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]:trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] -0.0002112
## Std. Error
## (Intercept) 0.1814706
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 0.0108489
## trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 0.0061506
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]:trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 0.0005622
## z value
## (Intercept) 3.666
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 3.306
## trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 0.296
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]:trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] -0.376
## Pr(>|z|)
## (Intercept) 0.000247
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 0.000947
## trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 0.767072
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]:trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 0.707240
##
## (Intercept) ***
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] ***
## trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]:trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 572.32 on 274 degrees of freedom
## Residual deviance: 539.30 on 271 degrees of freedom
## AIC: 1307.6
##
## Number of Fisher Scoring iterations: 5anova(glm(cobol$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]~fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]*trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0], family = poisson))## Analysis of Deviance Table
##
## Model: poisson, link: log
##
## Response: cobol$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]
##
## Terms added sequentially (first to last)
##
##
## Df
## NULL
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 1
## trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 1
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]:trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 1
## Deviance
## NULL
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 32.880
## trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 0.007
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]:trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 0.141
## Resid. Df
## NULL 274
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 273
## trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 272
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]:trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 271
## Resid. Dev
## NULL 572.32
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 539.44
## trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 539.44
## fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0]:trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density != 0] 539.30plot(glm(cobol$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]~fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]*trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0], family = poisson))
boxplot(cobol$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]~fer$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0])
boxplot(cobol$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0]~trans$latest.plot$computed.values$density[cobol$latest.plot$computed.values$density!=0])
##
Location of Orphan and underrepresented genes
all.ogs<-all.ogs[grep("Pyrenodesmiaerodens",all.ogs$V5),]
foo<-strsplit(all.ogs$V5,", ")
# Get orphan genes
prots_not_ogs<-unlist(foo)
prots_not_ogs<-gsub("-T1","",prots_not_ogs)
prots_not_ogs<-genes2[!(rownames(genes2)%in%prots_not_ogs),]
# Get underrepresented genes
ogs_depth<-sapply(foo,length)
foo<-sapply(foo,FUN=function(x){x<-x[grep("Pyrenodesmiaerodens",x)]})
ogs_depth<-ogs_depth[sapply(foo,length)==1]
foo<-foo[sapply(foo,length)==1]
foo<-foo[ogs_depth<=4]
foo<-unlist(foo)
foo<-gsub("-T1","",foo)
foo<-genes2[(rownames(genes2)%in%foo),]
#Karioplot_both
prots_not_ogs<-makeGRangesFromDataFrame(prots_not_ogs,
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="scaffold",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
prots_og_4s<-makeGRangesFromDataFrame(foo,
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="scaffold",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)kp <- plotKaryotype(genome = pe.genome, plot.type= 2)
kpPlotRegions(kp, data=paste(lrar$Name,":",lrar$Start+1,"-",lrar$End+1,sep=""),data.panel = 2,
col=spectrum[3], r0=-0.35, r1=-0.1, avoid.overlapping=FALSE)
#kpPlotDensity(kp, ranges_genes2, col="#6001A655",data.panel = 1, r0=0, r1=1, window.size = 50000)
kpPlotDensity(kp, data=mobile_elements,data.panel = 2,col=grey(0.3), r0=0, r1=1,window.size=50000)
kpPlotDensity(kp,lost_genes, col=spectrum[10],data.panel = 2, r0=0, r1=2, window.size = 50000)
kpPlotDensity(kp, data=prots_og_4s,data.panel = 1,col="#6001A655", r0=0, r1=1,window.size=50000)
kpPlotDensity(kp, data=prots_not_ogs,data.panel = 1,col=spectrum[10], r0=0, r1=1.75,window.size=50000)
3.6 Compare subtelomeric regions and regions proximal to LRARs with the rest of the genome
lrar_flanks<-makeGRangesFromDataFrame(lrar,
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="Name",
start.field="Start",
end.field="End",
strand.field="strand",
starts.in.df.are.0based=FALSE)
lrar_flanks<-flank(lrar_flanks,30000,both=TRUE)
lrar_flanks<-reduce(lrar_flanks)
lrar_flanks<-GenomicRanges::intersect(lrar_flanks,pe.genome)
lrar_flanks_with_telomeres<-lrar_flanks
lrar_flanks<-GenomicRanges::setdiff(lrar_flanks,telomere_locs)
non_telomeric_regions<-suppressWarnings(c(telomere_locs,lrar_flanks))
non_telomeric_regions<-reduce(non_telomeric_regions)
non_telomeric_regions<-GenomicRanges::setdiff(pe.genome,non_telomeric_regions)
kp <- plotKaryotype(genome = pe.genome, plot.type= 1)
kpPlotRegions(kp, lrar_flanks,data.panel = 2,col=grey(0.3), r0=0, r1=-0.3, avoid.overlapping=FALSE)
kpPlotRegions(kp, non_telomeric_regions,data.panel = 2,col="#6001A655", r0=0.3, r1=0.6, avoid.overlapping=FALSE)
kpPlotRegions(kp, telomere_locs,data.panel = 2,col="#F9973E55", r0=0.6, r1=0.9, avoid.overlapping=FALSE)
# gene density
genes_density_nt<-kpPlotDensity(kp, subsetByOverlaps(ranges_genes2,non_telomeric_regions), col="#6001A655",data.panel = 1, r0=0, r1=1, window.size = 50000)
genes_density_t<-kpPlotDensity(kp, subsetByOverlaps(ranges_genes2,telomere_locs), col="#6001A655",data.panel = 1, r0=0, r1=1, window.size = 50000)
genes_density_r<-kpPlotDensity(kp, subsetByOverlaps(ranges_genes2,lrar_flanks), col="#6001A655",data.panel = 1, r0=0, r1=1, window.size = 50000)
# Lost gene density
lost_density_nt<-kpPlotDensity(kp, subsetByOverlaps(lost_genes,non_telomeric_regions), col=spectrum[10],data.panel = 1, r0=0, r1=1.5, window.size = 50000)
lost_density_t<-kpPlotDensity(kp, subsetByOverlaps(lost_genes,telomere_locs), col=spectrum[10],data.panel = 1, r0=0, r1=1.5, window.size = 50000)## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_21, scaffold_27, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).lost_density_r<-kpPlotDensity(kp, subsetByOverlaps(lost_genes,lrar_flanks), col=spectrum[10],data.panel = 1, r0=0, r1=1.5, window.size = 50000)
# Mobile element density
trans_density_nt<-kpPlotDensity(kp, subsetByOverlaps(mobile_elements,non_telomeric_regions), data.panel = 2, col=grey(0.3), r0=0, r1=1,window.size=50000)
trans_density_t<-kpPlotDensity(kp, subsetByOverlaps(mobile_elements,telomere_locs),data.panel = 2, col=grey(0.3), r0=0, r1=1,window.size=50000)
trans_density_r<-kpPlotDensity(kp, subsetByOverlaps(mobile_elements,lrar_flanks),data.panel = 2,col=grey(0.3), r0=0, r1=1,window.size=50000)
# Underrepresented gene density (orthologs in 1 or two more genomes)
under_density_nt<-kpPlotDensity(kp, subsetByOverlaps(prots_og_4s,non_telomeric_regions), data.panel = 2, col=grey(0.3), r0=0, r1=1,window.size=50000)
under_density_t<-kpPlotDensity(kp, subsetByOverlaps(prots_og_4s,telomere_locs),data.panel = 2, col=grey(0.3), r0=0, r1=1,window.size=50000)
under_density_r<-kpPlotDensity(kp, subsetByOverlaps(prots_og_4s,lrar_flanks),data.panel = 2,col=grey(0.3), r0=0, r1=1,window.size=50000)
# Orfan gene density
orfan_density_nt<-kpPlotDensity(kp, subsetByOverlaps(prots_not_ogs,non_telomeric_regions), data.panel = 2, col=grey(0.3), r0=0, r1=1,window.size=50000)
orfan_density_t<-kpPlotDensity(kp, subsetByOverlaps(prots_not_ogs,telomere_locs),data.panel = 2, col=grey(0.3), r0=0, r1=1,window.size=50000)
orfan_density_r<-kpPlotDensity(kp, subsetByOverlaps(prots_not_ogs,lrar_flanks),data.panel = 2,col=grey(0.3), r0=0, r1=1,window.size=50000)
#base.for.circos<-function(GENOME)
{
require(circlize)
#------------------
# Initialize
#------------------
circos.genomicInitialize(data.frame(names=names(GENOME),start=0,end=sapply(GENOME,length)),sector.names = c(1:36))
set_track_gap(gap = 0.01)
circos.genomicTrack(ylim=c(0,1), track.height=0.015,bg.col=NA,bg.border=TRUE,cell.padding=c(0,0,0,0))
for (i in names(GENOME))
{
foo<-lrar_flanks[lrar_flanks@seqnames==i,]
if (length(foo)>0)
{
circos.genomicRect(cbind(foo@ranges@start,foo@ranges@start+foo@ranges@width-1), sector.index = i,ytop = 1, ybottom = 0, col=colorinos.bipolar[1], border = NA)
}
foo<-telomere_locs[telomere_locs@seqnames==i,]
if (length(foo)>0)
{
circos.genomicRect(cbind(foo@ranges@start,foo@ranges@start+foo@ranges@width-1), sector.index = i,ytop = 1, ybottom = 0, col=colorinos.bipolar[4], border = NA)
}
}
circos.genomicTrack(ylim=c(0,1), track.height=0.015,bg.col=NA,bg.border=TRUE,cell.padding=c(0,0,0,0))
# First track LRAR
set_track_gap(gap = 0.02)
for (i in names(GENOME))
{
foo<-lrar[lrar$Name==i,]
if (dim(foo)[1]>0)
{
circos.genomicRect(foo[,c(2,3)], sector.index = i,ytop = 1, ybottom = 0, col=grey(.5), border = NA)
}
}
# Second track Density mobile elements
circos.genomicDensity(as.data.frame(mobile_elements),col = grey(0.5), count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
# Third Gipsy
circos.genomicDensity(as.data.frame(ltrgypsy),col = spectrum[5], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
#
circos.genomicDensity(as.data.frame(ltrcopia),col = spectrum[10], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
#
circos.genomicDensity(as.data.frame(ltrNgaro),col = spectrum[15], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
#
circos.genomicDensity(as.data.frame(dna1),col = spectrum[20], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
#
circos.genomicDensity(as.data.frame(helitron),col = spectrum[25], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
circos.genomicDensity(as.data.frame(repetitive_sequences),col = spectrum[27], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
#
}
fii<-base.for.circos(pe_genome)## Loading required package: circlize## ========================================
## circlize version 0.4.15
## CRAN page: https://cran.r-project.org/package=circlize
## Github page: https://github.com/jokergoo/circlize
## Documentation: https://jokergoo.github.io/circlize_book/book/
##
## If you use it in published research, please cite:
## Gu, Z. circlize implements and enhances circular visualization
## in R. Bioinformatics 2014.
##
## This message can be suppressed by:
## suppressPackageStartupMessages(library(circlize))
## ========================================##
## Attaching package: 'circlize'## The following object is masked from 'package:ape':
##
## degree
print(fii)## NULLannotations_complete<-read.delim("/Users/Fernando/Desktop/01_paper_sanger_drive/Pyrenodesmia_erodens.annotations.txt",row.names=1)
sec_clust<-makeGRangesFromDataFrame(genes2[genes.all$SecMet.Cluster!="",],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="scaffold",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
sec_met<-makeGRangesFromDataFrame(genes2[rownames(annotations_complete)[annotations_complete$Secreted!=""],],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="scaffold",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
cazymes<-makeGRangesFromDataFrame(genes2[rownames(annotations_complete)[annotations_complete$CAZyme!=""],],
keep.extra.columns=FALSE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="scaffold",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
base.for.circos<-function(GENOME)
{
require(circlize)
#------------------
# Initialize
#------------------
circos.genomicInitialize(data.frame(names=names(GENOME),start=0,end=sapply(GENOME,length)),sector.names = c(1:36))
set_track_gap(gap = 0.01)
circos.genomicTrack(ylim=c(0,1), track.height=0.015,bg.col=NA,bg.border=TRUE,cell.padding=c(0,0,0,0))
for (i in names(GENOME))
{
foo<-lrar_flanks[lrar_flanks@seqnames==i,]
if (length(foo)>0)
{
circos.genomicRect(cbind(foo@ranges@start,foo@ranges@start+foo@ranges@width-1), sector.index = i,ytop = 1, ybottom = 0, col=colorinos.bipolar[1], border = NA)
}
foo<-telomere_locs[telomere_locs@seqnames==i,]
if (length(foo)>0)
{
circos.genomicRect(cbind(foo@ranges@start,foo@ranges@start+foo@ranges@width-1), sector.index = i,ytop = 1, ybottom = 0, col=colorinos.bipolar[4], border = NA)
}
}
circos.genomicTrack(ylim=c(0,1), track.height=0.015,bg.col=NA,bg.border=TRUE,cell.padding=c(0,0,0,0))
# First track LRAR
set_track_gap(gap = 0.02)
for (i in names(GENOME))
{
foo<-lrar[lrar$Name==i,]
if (dim(foo)[1]>0)
{
circos.genomicRect(foo[,c(2,3)], sector.index = i,ytop = 1, ybottom = 0, col=grey(.5), border = NA)
}
}
# Second track Density genes
circos.genomicDensity(as.data.frame(ranges_genes2),col = spectrum[1], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
# Missing genes
circos.genomicDensity(as.data.frame(lost_genes),col = spectrum[5], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
# Small OGs
circos.genomicDensity(as.data.frame(prots_og_4s),col = spectrum[10], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
# Orphan genes
circos.genomicDensity(as.data.frame(prots_not_ogs),col = spectrum[15], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
#
circos.genomicDensity(as.data.frame(cazymes),col = spectrum[20], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
#
circos.genomicDensity(as.data.frame(sec_clust),col = spectrum[25], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
#
circos.genomicDensity(as.data.frame(sec_met),col = spectrum[27], count_by = "number", track.height = 0.05,cell.padding=c(0,0,0,0))
}
fii<-base.for.circos(pe_genome)
print(fii)## NULLkp <- plotKaryotype(genome = pe.genome, plot.type= 1)
#ltrgypsy
ltrgypsy_density_nt<-kpPlotDensity(kp, subsetByOverlaps(ltrgypsy,non_telomeric_regions), data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)
ltrgypsy_density_t<-kpPlotDensity(kp, subsetByOverlaps(ltrgypsy,telomere_locs),data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24, scaffold_31, scaffold_35, scaffold_36
## - in 'y': scaffold_33
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).ltrgypsy_density_r<-kpPlotDensity(kp, subsetByOverlaps(ltrgypsy,lrar_flanks),data.panel = 1,col=grey(0.3), r0=0, r1=1,window.size=50000)
#ltrcopia
ltrcopia_density_nt<-kpPlotDensity(kp, subsetByOverlaps(ltrcopia,non_telomeric_regions), data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)
ltrcopia_density_t<-kpPlotDensity(kp, subsetByOverlaps(ltrcopia,telomere_locs),data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24, scaffold_31, scaffold_35, scaffold_36
## - in 'y': scaffold_30
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).ltrcopia_density_r<-kpPlotDensity(kp, subsetByOverlaps(ltrcopia,lrar_flanks),data.panel = 1,col=grey(0.3), r0=0, r1=1,window.size=50000)
#ltrNgaro
ltrNgaro_density_nt<-kpPlotDensity(kp, subsetByOverlaps(ltrNgaro,non_telomeric_regions), data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)
ltrNgaro_density_t<-kpPlotDensity(kp, subsetByOverlaps(ltrNgaro,telomere_locs),data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_16, scaffold_2, scaffold_22, scaffold_32, scaffold_9
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).ltrNgaro_density_r<-kpPlotDensity(kp, subsetByOverlaps(ltrNgaro,lrar_flanks),data.panel = 1,col=grey(0.3), r0=0, r1=1,window.size=50000)
#dna1
dna1_density_nt<-kpPlotDensity(kp, subsetByOverlaps(dna1,non_telomeric_regions), data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)
dna1_density_t<-kpPlotDensity(kp, subsetByOverlaps(dna1,telomere_locs),data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24, scaffold_31, scaffold_36
## - in 'y': scaffold_12, scaffold_14, scaffold_25, scaffold_30, scaffold_32, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).dna1_density_r<-kpPlotDensity(kp, subsetByOverlaps(dna1,lrar_flanks),data.panel = 1,col=grey(0.3), r0=0, r1=1,window.size=50000)
#helitron
helitron_density_nt<-kpPlotDensity(kp, subsetByOverlaps(helitron,non_telomeric_regions), data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)
helitron_density_t<-kpPlotDensity(kp, subsetByOverlaps(helitron,telomere_locs),data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24, scaffold_31, scaffold_36
## - in 'y': scaffold_29, scaffold_30, scaffold_32
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).helitron_density_r<-kpPlotDensity(kp, subsetByOverlaps(helitron,lrar_flanks),data.panel = 1,col=grey(0.3), r0=0, r1=1,window.size=50000)
#repetitive_sequences
repetitive_sequences_density_nt<-kpPlotDensity(kp, subsetByOverlaps(repetitive_sequences,non_telomeric_regions), data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)
repetitive_sequences_density_t<-kpPlotDensity(kp, subsetByOverlaps(repetitive_sequences,telomere_locs),data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)
repetitive_sequences_density_r<-kpPlotDensity(kp, subsetByOverlaps(repetitive_sequences,lrar_flanks),data.panel = 1,col=grey(0.3), r0=0, r1=1,window.size=50000)
# cazyme density
cazymes_density_nt<-kpPlotDensity(kp, subsetByOverlaps(cazymes,non_telomeric_regions), data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)
cazymes_density_t<-kpPlotDensity(kp, subsetByOverlaps(cazymes,telomere_locs),data.panel = 1, col=grey(0.3), r0=0, r1=1,window.size=50000)## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_32, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).cazymes_density_r<-kpPlotDensity(kp, subsetByOverlaps(cazymes,lrar_flanks),data.panel = 1,col=grey(0.3), r0=0, r1=1,window.size=50000)
# secmet density
sec_met_density_nt<-kpPlotDensity(kp, subsetByOverlaps(sec_met,non_telomeric_regions), data.panel = 2, col=grey(0.3), r0=0, r1=1,window.size=50000)
sec_met_density_t<-kpPlotDensity(kp, subsetByOverlaps(sec_met,telomere_locs),data.panel = 2, col=grey(0.3), r0=0, r1=1,window.size=50000)## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).sec_met_density_r<-kpPlotDensity(kp, subsetByOverlaps(sec_met,lrar_flanks),data.panel = 2,col=grey(0.3), r0=0, r1=1,window.size=50000)
# clust density
sec_clust_density_nt<-kpPlotDensity(kp, subsetByOverlaps(sec_clust,non_telomeric_regions), data.panel = 2, col=grey(0.3), r0=0, r1=1,window.size=50000)
sec_clust_density_t<-kpPlotDensity(kp, subsetByOverlaps(sec_clust,telomere_locs),data.panel = 2, col=grey(0.3), r0=0, r1=1,window.size=50000)## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23
## - in 'y': scaffold_13, scaffold_15, scaffold_18, scaffold_19, scaffold_25, scaffold_32, scaffold_34, scaffold_8
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).sec_clust_density_r<-kpPlotDensity(kp, subsetByOverlaps(sec_clust,lrar_flanks),data.panel = 2,col=grey(0.3), r0=0, r1=1,window.size=50000)
###
Differences in gene density between Telomeric, Centromeric+LRAR flanking
regions and the rest of the genome
ranges_results<-NULL
for (REGION in c("general","telomeric","LRAR"))
{
if (REGION=="general")
{ranges2use<-non_telomeric_regions
}else if (REGION=="telomeric")
{ranges2use<-telomere_locs
}else if (REGION=="LRAR")
{ranges2use<-lrar_flanks
}
for (TYPE in c("gene_density","lost_genes","mobile_elements","ltrgypsy","ltrcopia","ltrNgaro","dna1","helitron","repetitive_sequences","small_ogs","orphan","cazymes","sec_clust","sec_met"))
{
if (REGION=="general"&TYPE=="gene_density")
{data2use<-genes_density_nt
}else if (REGION=="telomeric"&TYPE=="gene_density")
{data2use<-genes_density_t
}else if (REGION=="LRAR"&TYPE=="gene_density")
{data2use<-genes_density_r
} else if (REGION=="general"&TYPE=="lost_genes")
{data2use<-lost_density_nt
}else if (REGION=="telomeric"&TYPE=="lost_genes")
{data2use<-lost_density_t
}else if (REGION=="LRAR"&TYPE=="lost_genes")
{data2use<-lost_density_r
} else if (REGION=="general"&TYPE=="mobile_elements")
{data2use<-trans_density_nt
}else if (REGION=="telomeric"&TYPE=="mobile_elements")
{data2use<-trans_density_t
}else if (REGION=="LRAR"&TYPE=="mobile_elements")
{data2use<-trans_density_r
} else if (REGION=="general"&TYPE=="small_ogs")
{data2use<-under_density_nt
}else if (REGION=="telomeric"&TYPE=="small_ogs")
{data2use<-under_density_t
}else if (REGION=="LRAR"&TYPE=="small_ogs")
{data2use<-under_density_r
} else if (REGION=="general"&TYPE=="orphan")
{data2use<-orfan_density_nt
}else if (REGION=="telomeric"&TYPE=="orphan")
{data2use<-orfan_density_t
}else if (REGION=="LRAR"&TYPE=="orphan")
{data2use<-orfan_density_r
} else if (REGION=="general"&TYPE=="cazymes")
{data2use<-cazymes_density_nt
}else if (REGION=="telomeric"&TYPE=="cazymes")
{data2use<-cazymes_density_t
}else if (REGION=="LRAR"&TYPE=="cazymes")
{data2use<-cazymes_density_r
}else if (REGION=="general"&TYPE=="sec_met")
{data2use<-sec_met_density_nt
}else if (REGION=="telomeric"&TYPE=="sec_met")
{data2use<-sec_met_density_t
}else if (REGION=="LRAR"&TYPE=="sec_met")
{data2use<-sec_met_density_r
}else if (REGION=="general"&TYPE=="sec_clust")
{data2use<-sec_clust_density_nt
}else if (REGION=="telomeric"&TYPE=="sec_clust")
{data2use<-sec_clust_density_t
}else if (REGION=="LRAR"&TYPE=="sec_clust")
{data2use<-sec_clust_density_r
}else if (REGION=="general"&TYPE=="ltrgypsy")
{data2use<-ltrgypsy_density_nt
}else if (REGION=="telomeric"&TYPE=="ltrgypsy")
{data2use<-ltrgypsy_density_t
}else if (REGION=="LRAR"&TYPE=="ltrgypsy")
{data2use<-ltrgypsy_density_r
}else if (REGION=="general"&TYPE=="ltrcopia")
{data2use<-ltrcopia_density_nt
}else if (REGION=="telomeric"&TYPE=="ltrcopia")
{data2use<-ltrcopia_density_t
}else if (REGION=="LRAR"&TYPE=="ltrcopia")
{data2use<-ltrcopia_density_r
}else if (REGION=="general"&TYPE=="ltrNgaro")
{data2use<-ltrNgaro_density_nt
}else if (REGION=="telomeric"&TYPE=="ltrNgaro")
{data2use<-ltrNgaro_density_t
}else if (REGION=="LRAR"&TYPE=="ltrNgaro")
{data2use<-ltrNgaro_density_r
}else if (REGION=="general"&TYPE=="dna1")
{data2use<-dna1_density_nt
}else if (REGION=="telomeric"&TYPE=="dna1")
{data2use<-dna1_density_t
}else if (REGION=="LRAR"&TYPE=="dna1")
{data2use<-dna1_density_r
}else if (REGION=="general"&TYPE=="helitron")
{data2use<-helitron_density_nt
}else if (REGION=="telomeric"&TYPE=="helitron")
{data2use<-helitron_density_t
}else if (REGION=="LRAR"&TYPE=="helitron")
{data2use<-helitron_density_r
}else if (REGION=="general"&TYPE=="repetitive_sequences")
{data2use<-repetitive_sequences_density_nt
}else if (REGION=="telomeric"&TYPE=="repetitive_sequences")
{data2use<-repetitive_sequences_density_t
}else if (REGION=="LRAR"&TYPE=="repetitive_sequences")
{data2use<-repetitive_sequences_density_r
}
for (I in 1:length(ranges2use))
{
ranges_results<-rbind(ranges_results,cbind(REGION,TYPE,I,mean( data2use$latest.plot$computed.values$density[attr(findOverlaps(data2use$latest.plot$computed.values$windows,ranges2use[I]),"from")])))
}
}
}
ranges_results<-data.frame(region=factor(ranges_results[,1]),feature=factor(ranges_results[,2]),local=ranges_results[,3],density=as.numeric(ranges_results[,4]))3.6.0.1 Density of mobile elements
ggplot(ranges_results[ranges_results$feature=="mobile_elements",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Density of mobile_elements") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="mobile_elements","density"],ranges_results[ranges_results$feature=="mobile_elements","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "mobile_elements", "density"] and ranges_results[ranges_results$feature == "mobile_elements", "region"]
##
## general LRAR
## LRAR < 2e-16 -
## telomeric 1.2e-10 0.0045
##
## P value adjustment method: BH3.6.0.2 LTRgypsy
ggplot(ranges_results[ranges_results$feature=="ltrgypsy",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="LTR/Gypsy") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="ltrgypsy","density"],ranges_results[ranges_results$feature=="ltrgypsy","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "ltrgypsy", "density"] and ranges_results[ranges_results$feature == "ltrgypsy", "region"]
##
## general LRAR
## LRAR < 2e-16 -
## telomeric 1.3e-06 6.0e-07
##
## P value adjustment method: BH3.6.0.3 ltrcopia
ggplot(ranges_results[ranges_results$feature=="ltrcopia",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="LTR/Copia") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="ltrcopia","density"],ranges_results[ranges_results$feature=="ltrcopia","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "ltrcopia", "density"] and ranges_results[ranges_results$feature == "ltrcopia", "region"]
##
## general LRAR
## LRAR < 2e-16 -
## telomeric 5.5e-09 0.013
##
## P value adjustment method: BH3.6.0.4 ltrNgaro
ggplot(ranges_results[ranges_results$feature=="ltrNgaro",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="LTR/Ngaro") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="ltrNgaro","density"],ranges_results[ranges_results$feature=="ltrNgaro","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "ltrNgaro", "density"] and ranges_results[ranges_results$feature == "ltrNgaro", "region"]
##
## general LRAR
## LRAR 6.5e-07 -
## telomeric 4.5e-11 0.041
##
## P value adjustment method: BH3.6.0.5 dna1
ggplot(ranges_results[ranges_results$feature=="dna1",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="dna1") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="dna1","density"],ranges_results[ranges_results$feature=="dna1","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "dna1", "density"] and ranges_results[ranges_results$feature == "dna1", "region"]
##
## general LRAR
## LRAR 1.5e-06 -
## telomeric 0.014 0.162
##
## P value adjustment method: BH3.6.0.6 helitron
ggplot(ranges_results[ranges_results$feature=="helitron",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="helitron") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="helitron","density"],ranges_results[ranges_results$feature=="helitron","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "helitron", "density"] and ranges_results[ranges_results$feature == "helitron", "region"]
##
## general LRAR
## LRAR 2.5e-07 -
## telomeric 0.00033 0.38554
##
## P value adjustment method: BH3.6.0.7 repetitive_sequences
ggplot(ranges_results[ranges_results$feature=="repetitive_sequences",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="repetitive_sequences") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="repetitive_sequences","density"],ranges_results[ranges_results$feature=="repetitive_sequences","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "repetitive_sequences", "density"] and ranges_results[ranges_results$feature == "repetitive_sequences", "region"]
##
## general LRAR
## LRAR 0.0036 -
## telomeric 4.7e-08 1.9e-05
##
## P value adjustment method: BH4
5
5.0.0.1 Gene density
ggplot(ranges_results[ranges_results$feature=="gene_density",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Average Gene density per region") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="gene_density","density"],ranges_results[ranges_results$feature=="gene_density","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "gene_density", "density"] and ranges_results[ranges_results$feature == "gene_density", "region"]
##
## general LRAR
## LRAR 1.1e-07 -
## telomeric 0.00024 8.9e-16
##
## P value adjustment method: BH5.0.0.2 Loss of synteny, density of putative missing genes
ggplot(ranges_results[ranges_results$feature=="lost_genes",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Density of missing genes") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="lost_genes","density"],ranges_results[ranges_results$feature=="lost_genes","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "lost_genes", "density"] and ranges_results[ranges_results$feature == "lost_genes", "region"]
##
## general LRAR
## LRAR 0.00764 -
## telomeric 0.24775 0.00099
##
## P value adjustment method: BH5.0.0.3 Small Orthogroups, with three samples or less
ggplot(ranges_results[ranges_results$feature=="small_ogs",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Density of small OGs") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="small_ogs","density"],ranges_results[ranges_results$feature=="small_ogs","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "small_ogs", "density"] and ranges_results[ranges_results$feature == "small_ogs", "region"]
##
## general LRAR
## LRAR 0.67 -
## telomeric 2.5e-09 6.3e-08
##
## P value adjustment method: BH5.0.0.4 Density of orphan genes
ggplot(ranges_results[ranges_results$feature=="orphan",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Density of orphan genes") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="orphan","density"],ranges_results[ranges_results$feature=="orphan","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "orphan", "density"] and ranges_results[ranges_results$feature == "orphan", "region"]
##
## general LRAR
## LRAR 0.9965 -
## telomeric 0.0083 0.0083
##
## P value adjustment method: BH5.0.0.5 Density of cazyme genes
ggplot(ranges_results[ranges_results$feature=="cazymes",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Density of cazyme genes") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="cazymes","density"],ranges_results[ranges_results$feature=="cazymes","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "cazymes", "density"] and ranges_results[ranges_results$feature == "cazymes", "region"]
##
## general LRAR
## LRAR 0.075 -
## telomeric 1.0e-05 2.4e-09
##
## P value adjustment method: BH5.0.0.6 Density of secreted genes
ggplot(ranges_results[ranges_results$feature=="sec_met",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Density of sec_met genes") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="sec_met","density"],ranges_results[ranges_results$feature=="sec_met","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "sec_met", "density"] and ranges_results[ranges_results$feature == "sec_met", "region"]
##
## general LRAR
## LRAR 0.011 -
## telomeric 2.2e-09 7.0e-13
##
## P value adjustment method: BH5.0.0.7 Density of secondary metabolism clusters
ggplot(ranges_results[ranges_results$feature=="sec_clust",],aes(x=region,y=density,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Density of sec_clust genes") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results[ranges_results$feature=="sec_clust","density"],ranges_results[ranges_results$feature=="sec_clust","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results[ranges_results$feature == "sec_clust", "density"] and ranges_results[ranges_results$feature == "sec_clust", "region"]
##
## general LRAR
## LRAR 0.47 -
## telomeric 1.4e-08 3.6e-09
##
## P value adjustment method: BH5.1 Phylogenetic signal across the genome
%### Plotting all
%{r} %culo<-loci_trees[!sapply(loci_trees,FUN=function(x){is.monophyletic(unroot(x),c("Xanpa","Cafla"))})] %for (i in 1:length(culo)) %{ % p<-ggtree(culo[[i]]) + geom_tippoint(color=as.numeric(factor(mat[culo[[i]]$tip.label,2])),size=3) + %geom_tiplab(align=FALSE, linetype="dotted", linesize=.3, offset=0.1) %print(p) %} %
het<-c("Pyrenodesmiaerodens_003026-T1",
"Pyrenodesmiaerodens_008956-T1",
"Pyrenodesmiaerodens_002843-T1",
"Pyrenodesmiaerodens_008195-T1",
"Pyrenodesmiaerodens_006652-T1",
"Pyrenodesmiaerodens_007209-T1",
"Pyrenodesmiaerodens_007178-T1",
"Pyrenodesmiaerodens_001939-T1",
"Pyrenodesmiaerodens_006912-T1",
"Pyrenodesmiaerodens_001303-T1",
"Pyrenodesmiaerodens_008514-T1",
"Pyrenodesmiaerodens_007614-T1",
"Pyrenodesmiaerodens_005425-T1",
"Pyrenodesmiaerodens_003710-T1",
"Pyrenodesmiaerodens_006911-T1",
"Pyrenodesmiaerodens_003701-T1",
"Pyrenodesmiaerodens_009360-T1",
"Pyrenodesmiaerodens_001394-T1",
"Pyrenodesmiaerodens_006881-T1",
"Pyrenodesmiaerodens_004495-T1",
"Pyrenodesmiaerodens_004888-T1",
"Pyrenodesmiaerodens_006904-T1",
"Pyrenodesmiaerodens_006707-T1",
"Pyrenodesmiaerodens_003667-T1",
"Pyrenodesmiaerodens_007504-T1",
"Pyrenodesmiaerodens_007081-T1",
"Pyrenodesmiaerodens_003230-T1",
"Pyrenodesmiaerodens_000215-T1",
"Pyrenodesmiaerodens_004826-T1",
"Pyrenodesmiaerodens_008820-T1",
"Pyrenodesmiaerodens_000990-T1",
"Pyrenodesmiaerodens_004497-T1",
"Pyrenodesmiaerodens_001877-T1",
"Pyrenodesmiaerodens_008462-T1",
"Pyrenodesmiaerodens_004488-T1",
"Pyrenodesmiaerodens_008467-T1",
"Pyrenodesmiaerodens_004430-T1",
"Pyrenodesmiaerodens_001833-T1",
"Pyrenodesmiaerodens_007926-T1",
"Pyrenodesmiaerodens_008989-T1","Pyrenodesmiaerodens_008241-T1")
het<-genes2[gsub("-T1","",het),]5.2 Plot pairwise heatmaps
genes$scaffold<-factor(genes$scaffold)
for (SCAF in levels(genes$scaffold)[order(as.numeric(sapply(strsplit(levels(genes$scaffold),"_"),`[`,2)))])
{
distances_foo<-data.frame(melt(as.matrix(distances)[genes$scaffold==SCAF,genes$scaffold==SCAF]))
p<-ggplot(distances_foo, aes(x=Var1, y=Var2, fill=value) ) + geom_tile() + scale_fill_continuous(type = "viridis") + theme_bw() + labs (title=paste("Heatmap of pairwise clustering distances,",SCAF),x="",y="")
print(p)
}
5.2.1 Plot consensus tree topology per scaffold
for (SCAF in levels(genes$scaffold)[order(as.numeric(sapply(strsplit(levels(genes$scaffold),"_"),`[`,2)))])
{
consino<-consensus(loci_trees[genes[,1]==SCAF], p = 0.5, check.labels = TRUE)
#plot(consino,main=paste("Consensus Topology of cluster",i),tip.color=as.numeric(factor(mat[consino$tip.label,2])))
p<-ggtree(consino) + geom_tippoint(color=as.numeric(factor(mat[consino$tip.label,2])),size=3) + geom_tiplab(align=TRUE, linetype="dotted", linesize=.3, offset=8) + xlim(0,25) + labs (title=paste("Consensus topology,",SCAF),x="",y="")
print(p)
}
5.2.2 Plot overall consensus topology
#for (SCAF in levels(genes$scaffold)[order(as.numeric(sapply(strsplit(levels(genes$scaffold),"_"),`[`,2)))])
#{
# write.tree(loci_trees[genes[,1]==SCAF],paste("/Users/Fernando/Desktop/3_Phylogenomics/",SCAF,"arboles.tree",sep=""))
#}
library(phylotate)
cupo<-read_annotated("/Users/Fernando/Desktop/3_Phylogenomics/RAxML_MajorityRuleExtendedConsensusTree_IC.mre",format="newick")
p<-ggtree(cupo) + geom_tiplab(align=TRUE, linetype="dotted", linesize=.3, offset=8) + xlim(0,25) + labs (title="Extended Majority Rule Consensus annotated with TC and IC support values.",x="",y="") + geom_text(aes(label=cupo$node.distance.comment), hjust=1, vjust=-0.6)## Warning in fortify.phylo(data, ...): 'edge.length' contains NA values...
## ## setting 'edge.length' to NULL automatically when plotting the tree...print(p)## Warning: Removed 26 rows containing missing values (geom_text).
# + geom_tippoint(color=as.numeric(factor(mat[consino$tip.label,2])),size=3) 5.2.3 Use the consensus tree to summarize comparative genomic data
library(aplot)
info<-synopsis_backup
rownames(info)<-info$Species<-c("Xanpa","Cafla","Pyrenodesmiaerodens","PyrenodesmiaX2","PyrenodesmiaX3","PyrenodesmiaX4","PyrenodesmiaX5","PyrenodesmiaX6","PyrenodesmiaX7","PyrenodesmiaX8","PyrenodesmiaX9","PyrenodesmiaY1","PyrenodesmiaY2","PyrenodesmiaY3","PyrenodesmiaY4","PyrenodesmiaY5","PyrenodesmiaY6","PyrenodesmiaY7","PyrenodesmiaY8","PyrenodesmiaY9","PyrenodesmiaY10","PyrenodesmiaY11","PyrenodesmiaY12","PyrenodesmiaY13","PyrenodesmiaY14")
info$name_correct<-c("Xanthoria parietina",
"Gyalolechia flavorubescens",
"Pyrenodesmia erodens",
"Pyrenodesmia transcaspica X2",
"Pyrenodesmia variabilis X3",
"Pyrenodesmia chalybaea X4",
"Pyrenodesmia micromontana X5",
"Pyrenodesmia medit1 X6",
"Pyrenodesmia alociza X7",
"Pyrenodesmia circumalbata X8",
"Pyrenodesmia micromarina X9",
"Pyrenodesmia chaplybaea Y1",
"Pyrenodesmia variabilis Y2",
"Pyrenodesmia variabilis Y3",
"Pyrenodesmia variabilis Y4",
"Pyrenodesmia variabilis Y5",
"Pyrenodesmia sp. Y6",
"Pyrenodesmia alociza Y7",
"Pyrenodesmia albovariegata Y8",
"Pyrenodesmia alociza Y9",
"Pyrenodesmia circumalbata Y10",
"Pyrenodesmia alociza Y11",
"Pyrenodesmia cf. albopruinosa Y12",
"Pyrenodesmia medit1 Y13",
"Pyrenodesmia cf. micromarina Y14")
info$cluster<-c(NA,
NA,
4,
9,
8,
5,
1,
10,
2,
8,
6,
5,
9,
8,
8,
8,
6,
7,
9,
3,
8,
6,
1,
10,
6)
info<-info[cupo$tip.label,]
info$Percent.GC<-as.numeric(info$Percent.GC)
info$node<-1:25
info<-fortify(info)
#facet_plot(p,panel="Size",data=info,geom=geom_bar,mapping = aes (x=Percent.GC))
pfams<-read.csv("/Users/Fernando/Desktop/compare_all/pfam/pfam.results.csv",row.names = 1)
pfams_1<-pfams[,c("descriptions")]
pfams_2<-pfams[,!(colnames(pfams)%in%c("descriptions"))]
cazymes<-read.csv("/Users/Fernando/Desktop/compare_all/cazy/CAZyme.all.results.csv",row.names = 1)
merops<-read.csv("/Users/Fernando/Desktop/compare_all/merops/MEROPS.all.results.csv",row.names = 1)
cogs<-read.csv("/Users/Fernando/Desktop/compare_all/cogs/COGS.all.results.csv",row.names = 1)
interpro<-read.csv("/Users/Fernando/Desktop/compare_all/interpro/interproscan.results.csv",row.names = 1)
interpro_desc<-interpro$descriptions
interpro<-interpro[,!(colnames(interpro)%in%c("descriptions"))]
#
# Process and obtain residual distributions
#
results_all<-list(
cazymes=apply(cazymes,1,FUN=function(x){(x[3]-mean(x[-3]))/sqrt(mean(x[-3]))}),
pfams=apply(pfams_2,1,FUN=function(x){(x[3]-median(x[-3]))/sqrt(median(x[-3]))}),
merops=apply(merops,1,FUN=function(x){(x[3]-median(x[-3]))/sqrt(median(x[-3]))}),
cogs=apply(cogs,1,FUN=function(x){(x[3]-median(x[-3]))/sqrt(median(x[-3]))}),
interpro=apply(interpro,1,FUN=function(x){(x[3]-median(x[-3]))/sqrt(median(x[-3]))})
)
results_all<-melt(results_all)
#
# TAKE OUT NAS DUE TO 0/0
#
results_all<-results_all[!is.na(results_all$value),]
results_all$L1<-factor(results_all$L1,levels=c("interpro","pfams","cazymes","cogs","merops"))5.2.4 Most PFAMs are equally present across all samples
The observed value of P.erodens is mostly equal to the median of the PFAm table occurrences (The residual Obs-Expected/sqrt(Expected) is zero).
ggplot(data.frame(results_all),aes(x=value,group=L1,fill=L1)) + geom_density(alpha=0.25) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])## Warning: Removed 83 rows containing non-finite values (stat_density).
Taking out all PFAMs with residuals different to zero we observe a higher frequency of negative than possitive residuals
results_all<-results_all[results_all$value!=0,]
ggplot(results_all[results_all$L1%in%c("cazymes","interpro","pfams"),],aes(x=value,group=L1,fill=L1)) + geom_density(aes(y = ..count..), alpha=0.5) + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(7,5,4,1,2,9,10,3)])## Warning: Removed 83 rows containing non-finite values (stat_density).
ipr<-apply(interpro,1,FUN=function(x){(x[3]-median(x[-3]))/sqrt(median(x[-3]))})
foo<-ipr!=0&!(is.na(ipr))&!(is.infinite(ipr))
foo<-data.frame(desc=interpro_desc[foo],res=ipr[foo])
foo<-foo[order(foo$res),]p<-ggtree(cupo) %<+% info + geom_tiplab(aes(label=name_correct),fontface=3,align=TRUE, linetype="dotted", linesize=.3, offset=3) + xlim(0,25) + geom_tippoint(aes(color=colorinos.bipolar[cluster]),size = 5) + theme(legend.position='none') + geom_text(aes(label=cupo$node.distance.comment), hjust=1, vjust=-0.6, size=2.5)## Warning in fortify.phylo(data, ...): 'edge.length' contains NA values...
## ## setting 'edge.length' to NULL automatically when plotting the tree...p2<-ggplot(data=info,aes(y=Percent.GC,x=Species))+geom_point(,col=colorinos.bipolar[1],pch=20,size=10)+coord_flip()+ theme_tree2() + theme(legend.position='none') + ylim(c(35,55))+geom_hline(yintercept = 50,col=colorinos.bipolar[6])
p3<-ggplot(data=info,aes(y=Assembly.Size,x=Species))+geom_col(aes(fill=colorinos.bipolar[cluster]),alpha=0.5)+coord_flip()+ theme_tree2() + theme(legend.position='none') + xlim(0,25)
p4<-ggplot(data=info,aes(y=Num.Genes,x=Species))+geom_col(aes(fill=colorinos.bipolar[cluster]),alpha=0.5)+coord_flip()+ theme_tree2() + theme(legend.position='none') + xlim(0,25)
p5<-ggplot(data=info,aes(y=Unique.Proteins,x=Species))+geom_col(aes(fill=colorinos.bipolar[cluster]),alpha=0.5)+coord_flip()+ theme_tree2() + theme(legend.position='none') + xlim(0,25)
p6<-ggplot(data=info,aes(y=Scaffold.N50,x=Species))+geom_col(aes(fill=colorinos.bipolar[cluster]),alpha=0.5)+coord_flip()+ theme_tree2() + theme(legend.position='none') + xlim(0,25)p2 %>% insert_left(p,width = 2) %>% insert_right(p3 +scale_y_reverse(),width = 0.5) %>% insert_right(p6,width = 0.5) %>%insert_right(p4 +scale_y_reverse(),width = 0.5) %>%insert_right(p5,width = 0.5)## Warning: Removed 26 rows containing missing values (geom_text).
5.3 Phylogenetic concordance between loci
logfile<-NULL
swindow<-NULL
plots<-list()
limite<-length(pe_genome[[1]])/1000
step=20
for (SCAF in levels(genes$scaffold)[order(as.numeric(sapply(strsplit(levels(genes$scaffold),"_"),`[`,2)))])
{
foo.dist<-as.matrix(distances)[genes$scaffold==SCAF,genes$scaffold==SCAF]
foo.loc<-as.numeric(as.character(genes$start[genes$scaffold==SCAF]))/1000
if(dim(foo.dist)[1]>=21)
{
for (i in 1:(dim(foo.dist)[1]-step))
{
swindow<-c(swindow,mean(foo.dist[c(i:(i+step)),c(i:(i+step))]))
}
logfile<-rbind(logfile,cbind(swindow,foo.loc[1:length(swindow)],as.numeric(sapply(strsplit(SCAF,"_"),`[`,2))))
culo<-lrar[lrar$Name==SCAF,]
#culo2<-rip[lrar$Name==SCAF,]
p<-ggplot(
data.frame(mean_dist=swindow,x=foo.loc[1:length(swindow)]),
aes(x=x, y=mean_dist, color=mean_dist)) + xlim(c(0,limite)) + ylim(c(2.5,12.5)) +
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=2.5,ymax=12.5,alpha = .3,fill = spectrum[1]) +
geom_point(size=0.5) +
geom_step() +
scale_color_continuous(type = "viridis", limits = range(2.5, 12.5))+
theme_bw() +
labs (title=paste("Sliding window of clustering distances across",SCAF),x="location",y="clustering distance")
if (length(unlist(het[het[,1]==SCAF,]))!=0)
{
plots[[SCAF]]<-p+geom_vline(xintercept = as.numeric(as.character(het[het[,1]==SCAF,2]))/1000, linetype = "longdash")+ theme(legend.position = "none")
}else{
plots[[SCAF]]<-p + theme(legend.position = "none")
}
}
#annotate("path",x=culo2$Start[order(culo2$Start)]/1000,y=culo2$GC.Content[order(culo2$Start)]/10, ymax=15, linetype=3, color = spectrum[2]) +
swindow<-NULL
}
logfile_distances<-logfilepempty<-list()
for (SCAF in c("scaffold_20","scaffold_21","scaffold_25","scaffold_31","scaffold_32","scaffold_33","scaffold_34","scaffold_35","scaffold_36"))
{
culo<-lrar[lrar$Name==SCAF,]
pempty[[SCAF]]<-ggplot(
data.frame(mean_dist=c(5,5,5),x=c(0,1000,10000)),
aes(x=x, y=mean_dist, color=mean_dist)) + xlim(c(0,limite)) + ylim(c(2.5,12.5))+theme_bw()+
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=2.5,ymax=12.5,alpha = .3,fill = spectrum[1])+
labs (title=paste("Not enough single copy orthologs were found on ",SCAF),x="location",y="clustering distance")
}
plots[[1]]/plots[[5]]/plots[[9]]/plots[[13]]/plots[[17]]/pempty[[2]]/pempty[[3]]/plots[[26]]/pempty[[6]]|
plots[[2]]/plots[[6]]/plots[[10]]/plots[[14]]/plots[[18]]/plots[[20]]/plots[[23]]/plots[[27]]/pempty[[7]]|
plots[[3]]/plots[[7]]/plots[[11]]/plots[[15]]/plots[[19]]/plots[[21]]/plots[[24]]/pempty[[4]]/pempty[[8]]|
plots[[4]]/plots[[8]]/plots[[12]]/plots[[16]]/pempty[[1]]/plots[[22]]/plots[[25]]/pempty[[5]]/pempty[[9]]## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?
5.4 Mapping dN/dS ratios along the genome
5.4.1 Sliding window of dN/dS
logfile<-NULL
swindow<-NULL
step=20
foo.genes<-genes[rownames(ogs),]
plots<-list()
limite<-length(pe_genome[[1]])/1000
for (SCAF in levels(genes$scaffold)[order(as.numeric(sapply(strsplit(levels(genes$scaffold),"_"),`[`,2)))])
{
foo.dnds<-ogs$dn_ds[foo.genes$scaffold==SCAF]
foo.loc<-as.numeric(as.character(foo.genes$start[foo.genes$scaffold==SCAF]))/1000
if(length(foo.dnds)>=21)
{
for (i in 1:(length(foo.dnds)-step))
{
swindow<-c(swindow,mean(foo.dnds[c(i:(i+step))]))
}
logfile<-rbind(logfile,cbind(swindow,foo.loc[1:length(swindow)],as.numeric(sapply(strsplit(SCAF,"_"),`[`,2))))
culo<-lrar[lrar$Name==SCAF,]
p<-ggplot(
data.frame(mean_dnds=swindow,x=foo.loc[1:length(swindow)]),
aes(x=x, y=mean_dnds, color=mean_dnds)) +
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0.05,ymax=0.25,alpha =.1,fill = spectrum[1]) +
geom_point(size=2) +
geom_step() +
scale_color_continuous(type = "viridis", limits = range(0.07,0.22)) +
xlim(c(0,limite)) + ylim(c(0.05,0.25)) +
theme_bw() +
labs (title=paste("Sliding window of dN/dS",SCAF),x="location",y="clustering distance")
if (length(unlist(het[het[,1]==SCAF,]))!=0)
{
plots[[SCAF]]<- p + geom_vline(xintercept = as.numeric(as.character(het[het[,1]==SCAF,2]))/1000, linetype = "longdash")+ theme(legend.position = "none")
}else{
plots[[SCAF]]<-p + theme(legend.position = "none")
}
}
swindow<-NULL
}
logfile_dnds<-logfile#, fig.width=22,fig.height=17}
pempty<-list()
for (SCAF in c("scaffold_20","scaffold_21","scaffold_25","scaffold_31","scaffold_32","scaffold_33","scaffold_34","scaffold_35","scaffold_36"))
{
culo<-lrar[lrar$Name==SCAF,]
pempty[[SCAF]]<-ggplot(
data.frame(mean_dist=c(5,5,5),x=c(0,1000,10000)),
aes(x=x, y=mean_dist, color=mean_dist)) + xlim(c(0,limite)) + ylim(c(0.05,0.25))+theme_bw()+
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0.05,ymax=0.25,alpha = .3,fill = spectrum[1])+
labs (title=paste("Not enough single copy orthologs were found on ",SCAF),x="location",y="clustering distance")
}
#plots[[1]]/plots[[5]]/plots[[9]]/plots[[13]]/plots[[17]]/pempty[[2]]/pempty[[3]]/plots[[26]]/pempty[[6]]|
#plots[[2]]/plots[[6]]/plots[[10]]/plots[[14]]/plots[[18]]/plots[[20]]/plots[[23]]/plots[[27]]/pempty[[7]]|
#plots[[3]]/plots[[7]]/plots[[11]]/plots[[15]]/plots[[19]]/plots[[21]]/plots[[24]]/pempty[[4]]/pempty[[8]]|
#plots[[4]]/plots[[8]]/plots[[12]]/plots[[16]]/pempty[[1]]/plots[[22]]/plots[[25]]/pempty[[5]]/pempty[[9]]
lapply(plots,print)
## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?
## $scaffold_1
##
## $scaffold_2
##
## $scaffold_3
##
## $scaffold_4
##
## $scaffold_5
##
## $scaffold_6
##
## $scaffold_7
##
## $scaffold_8
##
## $scaffold_9
##
## $scaffold_10
##
## $scaffold_11
##
## $scaffold_12
##
## $scaffold_13
##
## $scaffold_14
##
## $scaffold_15
##
## $scaffold_16
##
## $scaffold_17
##
## $scaffold_18
##
## $scaffold_19
##
## $scaffold_22
##
## $scaffold_23
##
## $scaffold_24
##
## $scaffold_26
##
## $scaffold_27
##
## $scaffold_28
##
## $scaffold_29
##
## $scaffold_30## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?
5.4.2 Plot of dN/dS values per ortholog, not on a sliding window.
logfile<-NULL
swindow<-NULL
foo.genes<-genes[rownames(ogs),]
plots<-list()
limite<-length(pe_genome[[1]])/1000
for (SCAF in levels(genes$scaffold)[order(as.numeric(sapply(strsplit(levels(genes$scaffold),"_"),`[`,2)))])
{
culo<-lrar[lrar$Name==SCAF,]
foo.dnds<-ogs$dn_ds[foo.genes$scaffold==SCAF]
foo.loc<-as.numeric(as.character(foo.genes$start[foo.genes$scaffold==SCAF]))/1000
p<-ggplot(
data.frame(dnds=foo.dnds,x=foo.loc),
aes(x=x, y=dnds, color=dnds)) +
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0,ymax=1,alpha =.1,fill = spectrum[1]) +
geom_point(size=2) +
geom_step() +
scale_color_continuous(type = "viridis", limits = range(0,1)) +
xlim(c(0,limite)) + ylim(c(0,1)) +
theme_bw() +
labs (title=paste("Sliding window of dN/dS",SCAF),x="location",y="clustering distance")
if (length(unlist(het[het[,1]==SCAF,]))!=0)
{
plots[[SCAF]]<- p + geom_vline(xintercept = as.numeric(as.character(het[het[,1]==SCAF,2]))/1000, linetype = "longdash") + theme(legend.position = "none")
}else{
plots[[SCAF]]<-p + theme(legend.position = "none")
}
swindow<-NULL
}pempty<-list()
for (SCAF in c("scaffold_20","scaffold_21","scaffold_25","scaffold_31","scaffold_32","scaffold_33","scaffold_34","scaffold_35","scaffold_36"))
{
culo<-lrar[lrar$Name==SCAF,]
pempty[[SCAF]]<-ggplot(
data.frame(mean_dist=c(5,5,5),x=c(0,1000,10000)),
aes(x=x, y=mean_dist, color=mean_dist)) + xlim(c(0,limite)) + ylim(c(0,1))+theme_bw()+
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0,ymax=1,alpha = .3,fill = spectrum[1])+
labs (title=paste("Not enough single copy orthologs were found on ",SCAF),x="location",y="clustering distance")
}
plots[[1]]/plots[[5]]/plots[[9]]/plots[[13]]/plots[[17]]/pempty[[2]]/pempty[[3]]/plots[[26]]/pempty[[6]]|
plots[[2]]/plots[[6]]/plots[[10]]/plots[[14]]/plots[[18]]/plots[[20]]/plots[[23]]/plots[[27]]/pempty[[7]]|
plots[[3]]/plots[[7]]/plots[[11]]/plots[[15]]/plots[[19]]/plots[[21]]/plots[[24]]/pempty[[4]]/pempty[[8]]|
plots[[4]]/plots[[8]]/plots[[12]]/plots[[16]]/pempty[[1]]/plots[[22]]/plots[[25]]/pempty[[5]]/pempty[[9]]
###
Average LRT M1/M2 (M1 = Almost Neutral, M2 = Positive selection) over a
sliding window
logfile<-NULL
swindow<-NULL
step=20
foo.genes<-genes[rownames(ogs),]
plots<-list()
limite<-length(pe_genome[[1]])/1000
for (SCAF in levels(genes$scaffold)[order(as.numeric(sapply(strsplit(levels(genes$scaffold),"_"),`[`,2)))])
{
foo.dnds<-ogs$uno[foo.genes$scaffold==SCAF]
foo.loc<-as.numeric(as.character(foo.genes$start[foo.genes$scaffold==SCAF]))/1000
if(length(foo.dnds)>=21)
{
for (i in 1:(length(foo.dnds)-step))
{
swindow<-c(swindow,mean(foo.dnds[c(i:(i+step))]))
}
logfile<-rbind(logfile,cbind(swindow,foo.loc[1:length(swindow)],as.numeric(sapply(strsplit(SCAF,"_"),`[`,2))))
culo<-lrar[lrar$Name==SCAF,]
p<-ggplot(
data.frame(mean_dnds=swindow,x=foo.loc[1:length(swindow)]),
aes(x=x, y=mean_dnds, color=mean_dnds)) +
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0.7,ymax=1,alpha =.1,fill = spectrum[1]) +
geom_point(size=2) +
geom_step() +
scale_color_continuous(type = "viridis", limits = range(0.70,1)) +
xlim(c(0,limite)) + ylim(c(0.7,1)) +
theme_bw() +
labs (title=paste("Sliding window of M1/M2",SCAF),x="location",y="clustering distance")
if (length(unlist(het[het[,1]==SCAF,]))!=0)
{
plots[[SCAF]]<- p + geom_vline(xintercept = as.numeric(as.character(het[het[,1]==SCAF,2]))/1000, linetype = "longdash") + theme(legend.position = "none")
}else{
plots[[SCAF]]<-p + theme(legend.position = "none")
}
}
swindow<-NULL
}
logfile_m1m2<-logfilepempty<-list()
for (SCAF in c("scaffold_20","scaffold_21","scaffold_25","scaffold_31","scaffold_32","scaffold_33","scaffold_34","scaffold_35","scaffold_36"))
{
culo<-lrar[lrar$Name==SCAF,]
pempty[[SCAF]]<-ggplot(
data.frame(mean_dist=c(5,5,5),x=c(0,1000,10000)),
aes(x=x, y=mean_dist, color=mean_dist)) + xlim(c(0,limite)) + ylim(c(0.7,1))+theme_bw()+
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0.7,ymax=1,alpha = .3,fill = spectrum[1])+
labs (title=paste("Not enough single copy orthologs were found on ",SCAF),x="location",y="clustering distance")
}
plots[[1]]/plots[[5]]/plots[[9]]/plots[[13]]/plots[[17]]/pempty[[2]]/pempty[[3]]/plots[[26]]/pempty[[6]]|
plots[[2]]/plots[[6]]/plots[[10]]/plots[[14]]/plots[[18]]/plots[[20]]/plots[[23]]/plots[[27]]/pempty[[7]]|
plots[[3]]/plots[[7]]/plots[[11]]/plots[[15]]/plots[[19]]/plots[[21]]/plots[[24]]/pempty[[4]]/pempty[[8]]|
plots[[4]]/plots[[8]]/plots[[12]]/plots[[16]]/pempty[[1]]/plots[[22]]/plots[[25]]/pempty[[5]]/pempty[[9]]## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?
5.4.3 Orthologwise values for LRT M1/M2 (M1 = Almost Neutral, M2 = Positive selection)
logfile<-NULL
swindow<-NULL
foo.genes<-genes[rownames(ogs),]
plots<-list()
limite<-length(pe_genome[[1]])/1000
for (SCAF in levels(genes$scaffold)[order(as.numeric(sapply(strsplit(levels(genes$scaffold),"_"),`[`,2)))])
{
culo<-lrar[lrar$Name==SCAF,]
foo.dnds<-ogs$uno[foo.genes$scaffold==SCAF]
foo.loc<-as.numeric(as.character(foo.genes$start[foo.genes$scaffold==SCAF]))/1000
p<-ggplot(
data.frame(dnds=foo.dnds,x=foo.loc),
aes(x=x, y=dnds, color=dnds)) +
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0,ymax=1,alpha =.1,fill = spectrum[1]) +
geom_point(size=2) +
geom_step() +
scale_color_continuous(type = "viridis", limits = range(0,1)) +
xlim(c(0,limite)) + ylim(c(0,1)) +
theme_bw() +
labs (title=paste("LRT M1/M2",SCAF),x="location",y="clustering distance")
if (length(unlist(het[het[,1]==SCAF,]))!=0)
{
plots[[SCAF]]<- p + geom_vline(xintercept = as.numeric(as.character(het[het[,1]==SCAF,2]))/1000, linetype = "longdash") + theme(legend.position = "none")
}else{
plots[[SCAF]]<-p + theme(legend.position = "none")
}
swindow<-NULL
}pempty<-list()
for (SCAF in c("scaffold_20","scaffold_21","scaffold_25","scaffold_31","scaffold_32","scaffold_33","scaffold_34","scaffold_35","scaffold_36"))
{
culo<-lrar[lrar$Name==SCAF,]
pempty[[SCAF]]<-ggplot(
data.frame(mean_dist=c(5,5,5),x=c(0,1000,10000)),
aes(x=x, y=mean_dist, color=mean_dist)) + xlim(c(0,limite)) + ylim(c(0,1))+theme_bw()+
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0,ymax=1,alpha = .3,fill = spectrum[1])+
labs (title=paste("Not enough single copy orthologs were found on ",SCAF),x="location",y="clustering distance")
}
plots[[1]]/plots[[5]]/plots[[9]]/plots[[13]]/plots[[17]]/pempty[[2]]/pempty[[3]]/plots[[26]]/pempty[[6]]|
plots[[2]]/plots[[6]]/plots[[10]]/plots[[14]]/plots[[18]]/plots[[20]]/plots[[23]]/plots[[27]]/pempty[[7]]|
plots[[3]]/plots[[7]]/plots[[11]]/plots[[15]]/plots[[19]]/plots[[21]]/plots[[24]]/pempty[[4]]/pempty[[8]]|
plots[[4]]/plots[[8]]/plots[[12]]/plots[[16]]/pempty[[1]]/plots[[22]]/plots[[25]]/pempty[[5]]/pempty[[9]]
5.4.4 Sliding window of LTR M7/M8
logfile<-NULL
swindow<-NULL
step=20
foo.genes<-genes[rownames(ogs),]
plots<-list()
limite<-length(pe_genome[[1]])/1000
for (SCAF in levels(genes$scaffold)[order(as.numeric(sapply(strsplit(levels(genes$scaffold),"_"),`[`,2)))])
{
foo.dnds<-ogs$dos[foo.genes$scaffold==SCAF]
foo.loc<-as.numeric(as.character(foo.genes$start[foo.genes$scaffold==SCAF]))/1000
if(length(foo.dnds)>=21)
{
for (i in 1:(length(foo.dnds)-step))
{
swindow<-c(swindow,mean(foo.dnds[c(i:(i+step))]))
}
logfile<-rbind(logfile,cbind(swindow,foo.loc[1:length(swindow)],as.numeric(sapply(strsplit(SCAF,"_"),`[`,2))))
culo<-lrar[lrar$Name==SCAF,]
p<-ggplot(
data.frame(mean_dnds=swindow,x=foo.loc[1:length(swindow)]),
aes(x=x, y=mean_dnds, color=mean_dnds)) +
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0.05,ymax=0.61,alpha =.1,fill = spectrum[1]) +
geom_point(size=2) +
geom_step() +
scale_color_continuous(type = "viridis", limits = range(0.05,0.61)) +
xlim(c(0,limite)) + ylim(c(0.05,0.61)) +
theme_bw() +
labs (title=paste("Sliding window of M1/M2",SCAF),x="location",y="clustering distance")
if (length(unlist(het[het[,1]==SCAF,]))!=0)
{
plots[[SCAF]]<- p + geom_vline(xintercept = as.numeric(as.character(het[het[,1]==SCAF,2]))/1000, linetype = "longdash") + theme(legend.position = "none")
}else{
plots[[SCAF]]<-p + theme(legend.position = "none")
}
}
swindow<-NULL
}
logfile_m7m8<-logfilepempty<-list()
for (SCAF in c("scaffold_20","scaffold_21","scaffold_25","scaffold_31","scaffold_32","scaffold_33","scaffold_34","scaffold_35","scaffold_36"))
{
culo<-lrar[lrar$Name==SCAF,]
pempty[[SCAF]]<-ggplot(
data.frame(mean_dist=c(5,5,5),x=c(0,1000,10000)),
aes(x=x, y=mean_dist, color=mean_dist)) + xlim(c(0,limite)) + ylim(c(0.7,1))+theme_bw()+
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0.05,ymax=0.61,alpha = .3,fill = spectrum[1])+
labs (title=paste("Not enough single copy orthologs were found on ",SCAF),x="location",y="clustering distance")
}
plots[[1]]/plots[[5]]/plots[[9]]/plots[[13]]/plots[[17]]/pempty[[2]]/pempty[[3]]/plots[[26]]/pempty[[6]]|
plots[[2]]/plots[[6]]/plots[[10]]/plots[[14]]/plots[[18]]/plots[[20]]/plots[[23]]/plots[[27]]/pempty[[7]]|
plots[[3]]/plots[[7]]/plots[[11]]/plots[[15]]/plots[[19]]/plots[[21]]/plots[[24]]/pempty[[4]]/pempty[[8]]|
plots[[4]]/plots[[8]]/plots[[12]]/plots[[16]]/pempty[[1]]/plots[[22]]/plots[[25]]/pempty[[5]]/pempty[[9]]## Warning: Removed 28 rows containing missing values (geom_rect).## Warning: Removed 13 rows containing missing values (geom_rect).## Warning: Removed 4 rows containing missing values (geom_rect).## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?## Warning: Removed 6 rows containing missing values (geom_rect).## Warning: Removed 14 rows containing missing values (geom_rect).## Warning: Removed 1 rows containing missing values (geom_rect).## Warning: Removed 10 rows containing missing values (geom_rect).
5.4.5 LRT M7/M8
logfile<-NULL
swindow<-NULL
foo.genes<-genes[rownames(ogs),]
plots<-list()
limite<-length(pe_genome[[1]])/1000
for (SCAF in levels(genes$scaffold)[order(as.numeric(sapply(strsplit(levels(genes$scaffold),"_"),`[`,2)))])
{
culo<-lrar[lrar$Name==SCAF,]
foo.dnds<-ogs$dos[foo.genes$scaffold==SCAF]
foo.loc<-as.numeric(as.character(foo.genes$start[foo.genes$scaffold==SCAF]))/1000
p<-ggplot(
data.frame(dnds=foo.dnds,x=foo.loc),
aes(x=x, y=dnds, color=dnds)) +
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0,ymax=1,alpha =.1,fill = spectrum[1]) +
geom_point(size=2) +
geom_step() +
scale_color_continuous(type = "viridis", limits = range(0,1)) +
xlim(c(0,limite)) + ylim(c(0,1)) +
theme_bw() +
labs (title=paste("Sliding window of M7/M8",SCAF),x="location",y="clustering distance")
if (length(unlist(het[het[,1]==SCAF,]))!=0)
{
plots[[SCAF]]<- p + geom_vline(xintercept = as.numeric(as.character(het[het[,1]==SCAF,2]))/1000, linetype = "longdash") + theme(legend.position = "none")
}else{
plots[[SCAF]]<-p+ theme(legend.position = "none")
}
swindow<-NULL
}pempty<-list()
for (SCAF in c("scaffold_20","scaffold_21","scaffold_25","scaffold_31","scaffold_32","scaffold_33","scaffold_34","scaffold_35","scaffold_36"))
{
culo<-lrar[lrar$Name==SCAF,]
pempty[[SCAF]]<-ggplot(
data.frame(mean_dist=c(5,5,5),x=c(0,1000,10000)),
aes(x=x, y=mean_dist, color=mean_dist)) + xlim(c(0,limite)) + ylim(c(0,1))+theme_bw()+
annotate("rect",xmin=culo$Start/1000,xmax=culo$End/1000,ymin=0,ymax=1,alpha = .3,fill = spectrum[1])+
labs (title=paste("Not enough single copy orthologs were found on ",SCAF),x="location",y="clustering distance")
}
plots[[1]]/plots[[5]]/plots[[9]]/plots[[13]]/plots[[17]]/pempty[[2]]/pempty[[3]]/plots[[26]]/pempty[[6]]|
plots[[2]]/plots[[6]]/plots[[10]]/plots[[14]]/plots[[18]]/plots[[20]]/plots[[23]]/plots[[27]]/pempty[[7]]|
plots[[3]]/plots[[7]]/plots[[11]]/plots[[15]]/plots[[19]]/plots[[21]]/plots[[24]]/pempty[[4]]/pempty[[8]]|
plots[[4]]/plots[[8]]/plots[[12]]/plots[[16]]/pempty[[1]]/plots[[22]]/plots[[25]]/pempty[[5]]/pempty[[9]]
###
Circos plot distance and dn/ds
ranges_phylodist<-makeGRangesFromDataFrame(data.frame(chr=paste("scaffold_",logfile_distances[,3],sep=""),start=logfile_distances[,2]*1000,end=(logfile_distances[,2]*1000)+100,dist=logfile_distances[,1]),
keep.extra.columns=TRUE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="chr",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
ranges_dnds<-makeGRangesFromDataFrame(data.frame(chr=paste("scaffold_",logfile_dnds[,3],sep=""),start=logfile_dnds[,2]*1000,end=(logfile_dnds[,2]*1000)+100,dist=logfile_dnds[,1]),
keep.extra.columns=TRUE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="chr",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
ranges_m1m2<-makeGRangesFromDataFrame(data.frame(chr=paste("scaffold_",logfile_m1m2[,3],sep=""),start=logfile_m1m2[,2]*1000,end=(logfile_m1m2[,2]*1000)+100,dist=logfile_m1m2[,1]),
keep.extra.columns=TRUE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="chr",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)
ranges_m7m8<-makeGRangesFromDataFrame(data.frame(chr=paste("scaffold_",logfile_m7m8[,3],sep=""),start=logfile_m7m8[,2]*1000,end=(logfile_m7m8[,2]*1000)+100,dist=logfile_m7m8[,1]),
keep.extra.columns=TRUE,
ignore.strand=FALSE,
seqinfo=NULL,
seqnames.field="chr",
start.field="start",
end.field="end",
strand.field="strand",
starts.in.df.are.0based=FALSE)shared.ogs<-strsplit(all.ogs$V5,split=", ")
shared.ogs<-melt(shared.ogs)
shared.ogs<-shared.ogs[grep("Pyrenodesmiaerodens",shared.ogs$value),]
shared.ogs$value<-as.character(shared.ogs$value)
shared.ogs$value<-gsub("-T1","",shared.ogs$value)
shared.ogs<-shared.ogs[shared.ogs[,2]%in%shared.ogs[,2][duplicated(shared.ogs[,2])],]
foo_uno<-unlist(strsplit(genes.all[shared.ogs$value,1],":"))
dim(foo_uno)<-c(2,length(foo_uno)/2)
foo_uno<-t(foo_uno)
shared.ogs<-cbind(shared.ogs,scaf=foo_uno[,1],start=sapply(strsplit(foo_uno[,2],"-"),`[`,1),end=sapply(strsplit(foo_uno[,2],"-"),`[`,2))
#shared.ogs$scaf<-as.numeric(gsub("scaffold_","",shared.ogs$scaf))base.for.circos<-function(GENOME,LINKS,LOST=lost_genes)
{
require(circlize)
#------------------
# Initialize
#------------------
circos.genomicInitialize(data.frame(names=names(GENOME),start=0,end=sapply(GENOME,length)),sector.names = c(1:36))
circos.genomicTrack(ylim=c(0,1), track.height=0.01,bg.col=NA,bg.border=TRUE,cell.padding=c(0,0,0,0))
# First track LRAR
for (i in names(GENOME))
{
foo<-lrar_flanks[lrar_flanks@seqnames==i,]
if (length(foo)>0)
{
circos.genomicRect(cbind(foo@ranges@start,foo@ranges@start+foo@ranges@width), sector.index = i,ytop = 1, ybottom = 0, col=colorinos.bipolar[1], border = NA)
}
foo<-telomere_locs[telomere_locs@seqnames==i,]
if (length(foo)>0)
{
circos.genomicRect(cbind(foo@ranges@start,foo@ranges@start+foo@ranges@width), sector.index = i,ytop = 1, ybottom = 0, col=colorinos.bipolar[4], border = NA)
}
}
#
circos.genomicTrack(ylim=c(2.5,12.5), track.height=0.15,bg.col=NA,bg.border=TRUE,cell.padding=c(0,0,0,0))
# First track
foo2<-as.data.frame(ranges_phylodist)
foo2<-cbind(foo2,
color=spectrum[round(30*(foo2$dist-min(foo2$dist))/(max(foo2$dist)-min(foo2$dist)))+1])
for (i in names(GENOME))
{
foo<-lrar[lrar$Name==i,]
foo3<-foo2[foo2$seqnames==i,]
foo3$end<-c(foo3$start[-1],foo3$start[dim(foo3)[1]])
if (dim(foo)[1]>0)
{
circos.genomicRect(foo[,c(2,3)], sector.index = i,ytop = 12.5, ybottom = 2.5, col=c("#6001A655"), border = NA)
if (dim(foo3)[1]>0)
{
circos.genomicPoints(foo3, value=foo3$dist, col = foo3$color, bg = foo3$color, count_by = "number", sector.index = i,pch=20, cex=0.25)
circos.segments(foo3$start,foo3$dist,foo3$end,c(foo3$dist[-1],foo3$dist[dim(foo3)[1]]), col = foo3$color, sector.index = i)
}
}
}
#
circos.genomicTrack(ylim=c(0.05,0.25), track.height=0.15,bg.col=NA,bg.border=TRUE,cell.padding=c(0,0,0,0))
# First track LRAR
foo2<-as.data.frame(ranges_dnds)
foo2<-cbind(foo2,
color=spectrum[round(30*(foo2$dist-min(foo2$dist))/(max(foo2$dist)-min(foo2$dist)))+1])
for (i in names(GENOME))
{
foo<-lrar[lrar$Name==i,]
foo3<-foo2[foo2$seqnames==i,]
if (dim(foo)[1]>0)
{
circos.genomicRect(foo[,c(2,3)], sector.index = i,ytop = 0.25, ybottom = 0.05, col=c("#6001A655"), border = NA)
if (dim(foo3)[1]>0)
{
circos.genomicPoints(foo3, value=foo3$dist, col = foo3$color, bg = foo3$color, count_by = "number", sector.index = i,pch=20, cex=0.25)
circos.segments(foo3$start,foo3$dist,foo3$end,c(foo3$dist[-1],foo3$dist[dim(foo3)[1]]), col = foo3$color, sector.index = i)
}
}
}
# third track links orthogroups
for (OG in levels(factor(LINKS$L1)))
{
foo4<-LINKS[LINKS$L1==OG,]
extent<-dim(foo4)[1]
for(i in c(1:(extent-1)))
{
for (j in c((i+1):extent))
{
if(foo4$scaf[i]!=foo4$scaf[j])
{
circos.link(foo4$scaf[i],c(as.numeric(foo4$start[i]),as.numeric(foo4$end[i])),foo4$scaf[j],c(as.numeric(foo4$start[j]),as.numeric(foo4$end[j])),col=c("#6001A655"))
}
}
}
}
}
base.for.circos(pe_genome,shared.ogs,lost_genes)## Note: 2 points are out of plotting region in sector 'scaffold_1', track
## '2'.## Note: 2 points are out of plotting region in sector 'scaffold_2', track
## '2'.## Note: 2 points are out of plotting region in sector 'scaffold_3', track
## '2'.## Note: 2 points are out of plotting region in sector 'scaffold_4', track
## '2'.## Note: 2 points are out of plotting region in sector 'scaffold_5', track
## '2'.## Note: 2 points are out of plotting region in sector 'scaffold_6', track
## '2'.## Note: 2 points are out of plotting region in sector 'scaffold_7', track
## '2'.## Note: 2 points are out of plotting region in sector 'scaffold_8', track
## '2'.## Note: 2 points are out of plotting region in sector 'scaffold_9', track
## '2'.## Note: 2 points are out of plotting region in sector 'scaffold_10',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_11',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_12',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_14',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_15',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_16',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_17',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_18',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_22',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_24',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_25',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_26',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_27',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_28',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_29',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_32',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_33',
## track '2'.## Note: 2 points are out of plotting region in sector 'scaffold_34',
## track '2'.
5.4.6 Is phylogenetic discordance correlated to the proliferation of transposable elements in the neighbouring LRARs?
ranges_results2<-NULL
for (REGION in c("general","telomeric","LRAR"))
{
if (REGION=="general")
{ranges2use<-non_telomeric_regions
}else if (REGION=="telomeric")
{ranges2use<-telomere_locs
}else if (REGION=="LRAR")
{ranges2use<-lrar_flanks
}
for (TYPE in c("distance","dnds","m1m2","m7m8"))
{
if (REGION=="general"&TYPE=="distance")
{data2use<-subsetByOverlaps(ranges_phylodist,non_telomeric_regions)
}else if (REGION=="telomeric"&TYPE=="distance")
{data2use<-subsetByOverlaps(ranges_phylodist,telomere_locs)
}else if (REGION=="LRAR"&TYPE=="distance")
{data2use<-subsetByOverlaps(ranges_phylodist,lrar_flanks)
} else if (REGION=="general"&TYPE=="dnds")
{data2use<-subsetByOverlaps(ranges_dnds,non_telomeric_regions)
}else if (REGION=="telomeric"&TYPE=="dnds")
{data2use<-subsetByOverlaps(ranges_dnds,telomere_locs)
}else if (REGION=="LRAR"&TYPE=="dnds")
{data2use<-subsetByOverlaps(ranges_dnds,lrar_flanks)
} else if (REGION=="general"&TYPE=="m1m2")
{data2use<-subsetByOverlaps(ranges_m1m2,non_telomeric_regions)
}else if (REGION=="telomeric"&TYPE=="m1m2")
{data2use<-subsetByOverlaps(ranges_m1m2,telomere_locs)
}else if (REGION=="LRAR"&TYPE=="m1m2")
{data2use<-subsetByOverlaps(ranges_m1m2,lrar_flanks)
} else if (REGION=="general"&TYPE=="m7m8")
{data2use<-subsetByOverlaps(ranges_m7m8,non_telomeric_regions)
}else if (REGION=="telomeric"&TYPE=="m7m8")
{data2use<-subsetByOverlaps(ranges_m7m8,telomere_locs)
}else if (REGION=="LRAR"&TYPE=="m7m8")
{data2use<-subsetByOverlaps(ranges_m7m8,lrar_flanks)
}
for (I in 1:length(ranges2use))
{
if (length(data2use$dist[attr(findOverlaps(data2use,ranges2use[I]),"from")])>0)
{
ranges_results2<-rbind(ranges_results2,cbind(REGION,TYPE,I,mean( data2use$dist[attr(findOverlaps(data2use,ranges2use[I]),"from")])))
}
}
}
}## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': scaffold_23, scaffold_24
## - in 'y': scaffold_20, scaffold_21, scaffold_25, scaffold_32, scaffold_33, scaffold_34
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).ranges_results2<-data.frame(region=factor(ranges_results2[,1]),feature=factor(ranges_results2[,2]),local=ranges_results2[,3],dist=as.numeric(ranges_results2[,4]))5.4.6.1 phylogenetic distance
ggplot(ranges_results2[ranges_results2$feature=="distance",],aes(x=region,y=dist,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Averaged phylogenetic distance between 20 neighbouring orthologs") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results2[ranges_results2$feature=="distance","dist"],ranges_results2[ranges_results2$feature=="distance","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results2[ranges_results2$feature == "distance", "dist"] and ranges_results2[ranges_results2$feature == "distance", "region"]
##
## general LRAR
## LRAR 0.2640 -
## telomeric 0.0104 0.0058
##
## P value adjustment method: BH5.4.6.2 dn/ds
ggplot(ranges_results2[ranges_results2$feature=="dnds",],aes(x=region,y=dist,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Averaged dn/ds between 20 neighbouring orthologs")+ theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results2[ranges_results2$feature=="dnds","dist"],ranges_results2[ranges_results2$feature=="dnds","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results2[ranges_results2$feature == "dnds", "dist"] and ranges_results2[ranges_results2$feature == "dnds", "region"]
##
## general LRAR
## LRAR 0.54 -
## telomeric 0.59 0.54
##
## P value adjustment method: BH5.4.6.3 m1/m2
ggplot(ranges_results2[ranges_results2$feature=="m1m2",],aes(x=region,y=dist,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Averaged phylogenetic distance between 20 neighbouring orthologs")+ theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results2[ranges_results2$feature=="m1m2","dist"],ranges_results2[ranges_results2$feature=="m1m2","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results2[ranges_results2$feature == "m1m2", "dist"] and ranges_results2[ranges_results2$feature == "m1m2", "region"]
##
## general LRAR
## LRAR 0.46 -
## telomeric 0.24 0.24
##
## P value adjustment method: BH5.4.6.4 m7/m8
ggplot(ranges_results2[ranges_results2$feature=="m7m8",],aes(x=region,y=dist,fill=region,z=feature))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Averaged phylogenetic distance between 20 neighbouring orthologs") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_results2[ranges_results2$feature=="m7m8","dist"],ranges_results2[ranges_results2$feature=="m7m8","region"],p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_results2[ranges_results2$feature == "m7m8", "dist"] and ranges_results2[ranges_results2$feature == "m7m8", "region"]
##
## general LRAR
## LRAR 0.329 -
## telomeric 0.057 0.034
##
## P value adjustment method: BH5.4.7 Is phylogenetic discordance correlated to the proliferation of transposable elements in the neighbouring LRARs?
#lrar_flanks_with_telomeres
ranges_lrar<-cbind(tabulate_rep_lrar[,1:4],mean_dist=0)
ranges_lrar$Start<-ranges_lrar$Start-50000
ranges_lrar$End<-ranges_lrar$End+50000
ranges_lrar$Start[ranges_lrar$Start<0]<-0
for (i in 1:dim(ranges_lrar)[1])
{
ranges_lrar[i,"mean_dist"]<-mean(
logfile_distances[logfile_distances[,3]==sapply(strsplit(ranges_lrar[i,1],"_"),`[`,2)&
logfile_distances[,2]>=ranges_lrar[i,2]/1000&logfile_distances[,2]<=ranges_lrar[i,3]/1000
,1])
}
#anova(lm(ranges_lrar$mean_dist~tabulate_rep_lrar[,14]*(tabulate_rep_lrar[,13]+tabulate_rep_lrar[,11])))
#foo_reg<-cbind(tabulate_rep_lrar,mean_dist = ranges_lrar$mean_dist)
foo_reg<-cbind(ranges_lrar,tabulate_rep_lrar[,10:19],mean_dist = ranges_lrar$mean_dist)
fit<-lm(mean_dist~`DNA/hAT-Ac`+`DNA/MULE-MuDR`+`Low_complexity`+`LTR/Copia`+`LTR/Gypsy`+`LTR/Ngaro`+`RC/Helitron`+`Simple_repeat`+`Unknown`+`Unspecified`,data = foo_reg)
summary(fit)##
## Call:
## lm(formula = mean_dist ~ `DNA/hAT-Ac` + `DNA/MULE-MuDR` + Low_complexity +
## `LTR/Copia` + `LTR/Gypsy` + `LTR/Ngaro` + `RC/Helitron` +
## Simple_repeat + Unknown + Unspecified, data = foo_reg)
##
## Residuals:
## Min 1Q Median 3Q Max
## -3.0039 -0.9938 0.0921 1.0380 3.8602
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 7.193e+00 1.837e-01 39.149 < 2e-16 ***
## `DNA/hAT-Ac` -2.126e+03 2.976e+03 -0.714 0.476
## `DNA/MULE-MuDR` -1.123e+04 7.146e+03 -1.572 0.117
## Low_complexity 3.818e+02 1.665e+03 0.229 0.819
## `LTR/Copia` 3.172e+02 6.876e+02 0.461 0.645
## `LTR/Gypsy` -8.054e+02 6.298e+02 -1.279 0.202
## `LTR/Ngaro` 7.217e+02 1.576e+03 0.458 0.647
## `RC/Helitron` -2.917e+02 1.165e+03 -0.250 0.803
## Simple_repeat -1.644e+02 5.668e+02 -0.290 0.772
## Unknown -1.219e+03 2.909e+02 -4.191 3.75e-05 ***
## Unspecified 2.286e+03 2.175e+03 1.051 0.294
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.349 on 274 degrees of freedom
## (250 observations deleted due to missingness)
## Multiple R-squared: 0.09912, Adjusted R-squared: 0.06624
## F-statistic: 3.015 on 10 and 274 DF, p-value: 0.00124anova(fit)## Analysis of Variance Table
##
## Response: mean_dist
## Df Sum Sq Mean Sq F value Pr(>F)
## `DNA/hAT-Ac` 1 1.02 1.0184 0.5595 0.455090
## `DNA/MULE-MuDR` 1 4.04 4.0374 2.2182 0.137538
## Low_complexity 1 0.19 0.1856 0.1020 0.749703
## `LTR/Copia` 1 0.09 0.0888 0.0488 0.825368
## `LTR/Gypsy` 1 12.55 12.5467 6.8935 0.009137 **
## `LTR/Ngaro` 1 0.77 0.7731 0.4247 0.515127
## `RC/Helitron` 1 2.88 2.8796 1.5821 0.209526
## Simple_repeat 1 0.30 0.2991 0.1643 0.685504
## Unknown 1 31.03 31.0327 17.0501 4.838e-05 ***
## Unspecified 1 2.01 2.0093 1.1039 0.294330
## Residuals 274 498.71 1.8201
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Mclust(ranges_lrar$mean_dist[!is.na(ranges_lrar$mean_dist)],1:10)## 'Mclust' model object: (E,2)
##
## Available components:
## [1] "call" "data" "modelName" "n"
## [5] "d" "G" "BIC" "loglik"
## [9] "df" "bic" "icl" "hypvol"
## [13] "parameters" "z" "classification" "uncertainty"ggplot(data.frame(lrars=ranges_lrar$mean_dist,class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Distance per LRAR groups") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])## Warning: Removed 250 rows containing non-finite values (stat_ydensity).## Warning: Removed 250 rows containing missing values (geom_point).
pairwise.wilcox.test(ranges_lrar$mean_dist,as.factor(grupos$classification),p.adjust.method = "BH")## Warning in wilcox.test.default(xi, xj, paired = paired, ...): cannot compute
## exact p-value with ties
## Warning in wilcox.test.default(xi, xj, paired = paired, ...): cannot compute
## exact p-value with ties
## Warning in wilcox.test.default(xi, xj, paired = paired, ...): cannot compute
## exact p-value with ties
## Warning in wilcox.test.default(xi, xj, paired = paired, ...): cannot compute
## exact p-value with ties
## Warning in wilcox.test.default(xi, xj, paired = paired, ...): cannot compute
## exact p-value with ties
## Warning in wilcox.test.default(xi, xj, paired = paired, ...): cannot compute
## exact p-value with ties
## Warning in wilcox.test.default(xi, xj, paired = paired, ...): cannot compute
## exact p-value with ties
## Warning in wilcox.test.default(xi, xj, paired = paired, ...): cannot compute
## exact p-value with ties
## Warning in wilcox.test.default(xi, xj, paired = paired, ...): cannot compute
## exact p-value with ties##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_lrar$mean_dist and as.factor(grupos$classification)
##
## 1 2 3 4 5
## 2 0.76 - - - -
## 3 0.81 0.99 - - -
## 4 0.17 0.17 0.17 - -
## 5 0.81 0.76 0.76 0.17 -
## 6 0.81 0.81 0.81 0.81 0.76
##
## P value adjustment method: BHgrupos<-Mclust(ranges_lrar$mean_dist[!is.na(ranges_lrar$mean_dist)],1:20)ggplot(data.frame(lrars=ranges_lrar$mean_dist[!is.na(ranges_lrar$mean_dist)],class=as.factor(grupos$classification)),aes(x=class,y=lrars,fill=class))+geom_violin(alpha=0.5)+geom_point(position = position_jitter(seed = 1, width = 0.2))+ labs (title="Distance per LRAR groups") + theme_bw() +scale_fill_discrete(type=colorinos.bipolar[c(6,7,5,8,4,1,2,9,10,3)])
pairwise.wilcox.test(ranges_lrar$mean_dist[!is.na(ranges_lrar$mean_dist)],as.factor(grupos$classification),p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: ranges_lrar$mean_dist[!is.na(ranges_lrar$mean_dist)] and as.factor(grupos$classification)
##
## 1
## 2 <2e-16
##
## P value adjustment method: BH